Starting phenix.real_space_refine
on Thu Feb  5 06:54:37 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9krl_62532/02_2026/9krl_62532_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9krl_62532/02_2026/9krl_62532.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.99
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9krl_62532/02_2026/9krl_62532.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9krl_62532/02_2026/9krl_62532.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9krl_62532/02_2026/9krl_62532_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9krl_62532/02_2026/9krl_62532_trim.cif"
  }
  resolution = 2.99
  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=  -0.001 sd=   0.090
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: 6
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      37      5.16       5
     C    4910      2.51       5
     N    1257      2.21       5
     O    1329      1.98       5
     H    7718      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 15252
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 15230
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 935, 15230
          Classifications: {'peptide': 935}
          Link IDs: {'PTRANS': 28, 'TRANS': 906}
          Chain breaks: 4
    Chain: "A"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 22
          Classifications: {'RNA': 1}
          Modifications used: {'rna3p': 1}
  Time building chain proxies: 2.57, per 1000 atoms: 0.17
  Number of scatterers: 15252
  At special positions: 0
  Unit cell: (80.3, 103.4, 147.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      37     16.00
     P       1     15.00
     O    1329      8.00
     N    1257      7.00
     C    4910      6.00
     H    7718      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.16
  Conformation dependent library (CDL) restraints added in 405.2 milliseconds
  

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1782

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 2 sheets defined
      72.2% alpha, 1.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 24 through 26
      No H-bonds generated for 'chain 'A' and resid 24 through 26'
    Processing helix  chain 'A' and resid 27 through 35
      removed outlier: 4.145A  pdb=" N   PHE A  31 " --> pdb=" O   LEU A  27 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 57
    Processing helix  chain 'A' and resid 58 through 74
      removed outlier: 3.944A  pdb=" N   ASP A  74 " --> pdb=" O   ARG A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 86
      removed outlier: 3.841A  pdb=" N   ILE A  85 " --> pdb=" O   THR A  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 104
      removed outlier: 4.111A  pdb=" N   TYR A  92 " --> pdb=" O   TYR A  88 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   ILE A  97 " --> pdb=" O   LEU A  93 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   PHE A  98 " --> pdb=" O   VAL A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 122
      removed outlier: 3.865A  pdb=" N   LYS A 115 " --> pdb=" O   ILE A 111 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   ILE A 116 " --> pdb=" O   PHE A 112 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ILE A 117 " --> pdb=" O   LEU A 113 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   ASN A 118 " --> pdb=" O   GLY A 114 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   TYR A 119 " --> pdb=" O   LYS A 115 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   PHE A 120 " --> pdb=" O   ILE A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 150
      removed outlier: 3.956A  pdb=" N   ASN A 132 " --> pdb=" O   SER A 128 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   THR A 133 " --> pdb=" O   VAL A 129 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ALA A 134 " --> pdb=" O   ALA A 130 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   THR A 142 " --> pdb=" O   ALA A 138 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   PHE A 143 " --> pdb=" O   THR A 139 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   CYS A 144 " --> pdb=" O   VAL A 140 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   THR A 145 " --> pdb=" O   LEU A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 179
      removed outlier: 4.176A  pdb=" N   TYR A 155 " --> pdb=" O   LEU A 151 " (cutoff:3.500A)
      removed outlier: 4.201A  pdb=" N   GLY A 163 " --> pdb=" O   VAL A 159 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   MET A 164 " --> pdb=" O   GLN A 160 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ARG A 165 " --> pdb=" O   CYS A 161 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   LEU A 166 " --> pdb=" O   ALA A 162 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   CYS A 171 " --> pdb=" O   ARG A 167 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   HIS A 172 " --> pdb=" O   VAL A 168 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   MET A 173 " --> pdb=" O   ALA A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 187
    Processing helix  chain 'A' and resid 190 through 200
      removed outlier: 3.927A  pdb=" N   LEU A 198 " --> pdb=" O   ILE A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 203
      No H-bonds generated for 'chain 'A' and resid 201 through 203'
    Processing helix  chain 'A' and resid 204 through 209
      removed outlier: 3.870A  pdb=" N   VAL A 208 " --> pdb=" O   LYS A 204 " (cutoff:3.500A)
      removed outlier: 4.396A  pdb=" N   THR A 209 " --> pdb=" O   PHE A 205 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 204 through 209'
    Processing helix  chain 'A' and resid 210 through 212
      No H-bonds generated for 'chain 'A' and resid 210 through 212'
    Processing helix  chain 'A' and resid 213 through 231
      Proline residue:  A 219  - end of helix
      removed outlier: 3.728A  pdb=" N   MET A 231 " --> pdb=" O   ALA A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 236
      No H-bonds generated for 'chain 'A' and resid 234 through 236'
    Processing helix  chain 'A' and resid 237 through 242
    Processing helix  chain 'A' and resid 246 through 281
      removed outlier: 3.734A  pdb=" N   CYS A 253 " --> pdb=" O   PRO A 249 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   PHE A 254 " --> pdb=" O   LEU A 250 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   SER A 260 " --> pdb=" O   LYS A 256 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   LEU A 261 " --> pdb=" O   LEU A 257 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   THR A 267 " --> pdb=" O   SER A 263 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   PHE A 268 " --> pdb=" O   LYS A 264 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   ARG A 272 " --> pdb=" O   PHE A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 290
      removed outlier: 3.970A  pdb=" N   MET A 288 " --> pdb=" O   ARG A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 326
      removed outlier: 4.481A  pdb=" N   PHE A 295 " --> pdb=" O   TRP A 291 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   LEU A 302 " --> pdb=" O   LEU A 298 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   ARG A 312 " --> pdb=" O   SER A 308 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   SER A 313 " --> pdb=" O   LYS A 309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 343
      removed outlier: 4.090A  pdb=" N   GLY A 343 " --> pdb=" O   TYR A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 350 through 390
      removed outlier: 3.617A  pdb=" N   ALA A 354 " --> pdb=" O   ARG A 350 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   LEU A 363 " --> pdb=" O   GLY A 359 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   THR A 364 " --> pdb=" O   ALA A 360 " (cutoff:3.500A)
      Proline residue:  A 370  - end of helix
      removed outlier: 3.721A  pdb=" N   ILE A 373 " --> pdb=" O   PHE A 369 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   GLU A 374 " --> pdb=" O   PRO A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 697 through 706
      removed outlier: 3.585A  pdb=" N   TYR A 701 " --> pdb=" O   GLY A 697 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 710 through 722
      removed outlier: 3.560A  pdb=" N   PHE A 714 " --> pdb=" O   HIS A 710 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   THR A 722 " --> pdb=" O   ILE A 718 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 723 through 744
      removed outlier: 3.710A  pdb=" N   ALA A 727 " --> pdb=" O   ALA A 723 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   ASP A 732 " --> pdb=" O   TYR A 728 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   LEU A 735 " --> pdb=" O   GLN A 731 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   MET A 744 " --> pdb=" O   ASN A 740 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 760 through 806
      removed outlier: 4.163A  pdb=" N   TYR A 764 " --> pdb=" O   ASP A 760 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   TYR A 768 " --> pdb=" O   TYR A 764 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   THR A 775 " --> pdb=" O   LEU A 771 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   VAL A 776 " --> pdb=" O   THR A 772 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   SER A 783 " --> pdb=" O   GLY A 779 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   SER A 793 " --> pdb=" O   VAL A 789 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   SER A 794 " --> pdb=" O   LEU A 790 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   ASN A 799 " --> pdb=" O   GLN A 795 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   LYS A 800 " --> pdb=" O   THR A 796 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 817 through 835
      removed outlier: 3.767A  pdb=" N   ILE A 821 " --> pdb=" O   PRO A 817 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   ILE A 829 " --> pdb=" O   PHE A 825 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 835 through 860
      removed outlier: 3.720A  pdb=" N   VAL A 850 " --> pdb=" O   THR A 846 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   VAL A 851 " --> pdb=" O   LEU A 847 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   GLY A 852 " --> pdb=" O   LEU A 848 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   VAL A 853 " --> pdb=" O   GLN A 849 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   VAL A 860 " --> pdb=" O   VAL A 856 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 861 through 866
    Processing helix  chain 'A' and resid 867 through 887
      removed outlier: 4.109A  pdb=" N   LEU A 871 " --> pdb=" O   PRO A 867 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   PHE A 875 " --> pdb=" O   LEU A 871 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   ILE A 876 " --> pdb=" O   GLY A 872 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   ARG A 880 " --> pdb=" O   ILE A 876 " (cutoff:3.500A)
      removed outlier: 4.804A  pdb=" N   THR A 885 " --> pdb=" O   TYR A 881 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 888 through 908
      Proline residue:  A 899  - end of helix
    Processing helix  chain 'A' and resid 911 through 917
      removed outlier: 3.511A  pdb=" N   TYR A 917 " --> pdb=" O   THR A 913 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 920 through 970
      removed outlier: 3.788A  pdb=" N   GLN A 924 " --> pdb=" O   GLU A 920 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   LEU A 933 " --> pdb=" O   ALA A 929 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   HIS A 934 " --> pdb=" O   HIS A 930 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   PHE A 948 " --> pdb=" O   THR A 944 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   ALA A 949 " --> pdb=" O   SER A 945 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   VAL A 950 " --> pdb=" O   ARG A 946 " (cutoff:3.500A)
      removed outlier: 4.328A  pdb=" N   ARG A 951 " --> pdb=" O   TRP A 947 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ILE A 955 " --> pdb=" O   ARG A 951 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   VAL A 960 " --> pdb=" O   CYS A 956 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 975 through 987
      removed outlier: 3.584A  pdb=" N   VAL A 979 " --> pdb=" O   ASP A 975 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   TYR A 985 " --> pdb=" O   LEU A 981 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   LEU A 987 " --> pdb=" O   LEU A 983 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 988 through 1014
      removed outlier: 4.203A  pdb=" N   MET A 992 " --> pdb=" O   THR A 988 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   SER A1000 " --> pdb=" O   CYS A 996 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   ALA A1001 " --> pdb=" O   VAL A 997 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   GLU A1002 " --> pdb=" O   ARG A 998 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   ILE A1008 " --> pdb=" O   GLU A1004 " (cutoff:3.500A)
      removed outlier: 5.024A  pdb=" N   SER A1009 " --> pdb=" O   ASN A1005 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   VAL A1010 " --> pdb=" O   MET A1006 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1083 through 1089
    Processing helix  chain 'A' and resid 1110 through 1115
    Processing helix  chain 'A' and resid 1142 through 1150
    Processing helix  chain 'A' and resid 1156 through 1161
      removed outlier: 3.962A  pdb=" N   GLU A1160 " --> pdb=" O   LYS A1156 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ASP A1161 " --> pdb=" O   GLU A1157 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1156 through 1161'
    Processing helix  chain 'A' and resid 1171 through 1175
    Processing helix  chain 'A' and resid 1178 through 1194
    Processing helix  chain 'A' and resid 1212 through 1223
      removed outlier: 3.650A  pdb=" N   PHE A1223 " --> pdb=" O   ILE A1219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1234 through 1238
    Processing helix  chain 'A' and resid 1257 through 1261
      removed outlier: 3.622A  pdb=" N   VAL A1260 " --> pdb=" O   GLU A1257 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 1064 through 1065
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1117 through 1120
      removed outlier: 3.564A  pdb=" N   SER A1118 " --> pdb=" O   ILE A1197 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ASP A1201 " --> pdb=" O   ILE A1120 " (cutoff:3.500A)

    406 hydrogen bonds defined for protein.
    1188 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: 2.89

  Time building geometry restraints manager: 1.67 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 7705
        1.03 -     1.23: 13
        1.23 -     1.42: 3186
        1.42 -     1.62: 4452
        1.62 -     1.81: 62
  Bond restraints: 15418
  Sorted by residual:
  bond pdb=" C3' CMP A1401 "
       pdb=" C4' CMP A1401 "
    ideal  model  delta    sigma   weight residual
    1.521  1.500  0.021 1.50e-02 4.44e+03 1.90e+00
  bond pdb=" C4  CMP A1401 "
       pdb=" C5  CMP A1401 "
    ideal  model  delta    sigma   weight residual
    1.490  1.468  0.022 2.00e-02 2.50e+03 1.18e+00
  bond pdb=" O5' CMP A1401 "
       pdb=" P   CMP A1401 "
    ideal  model  delta    sigma   weight residual
    1.593  1.607 -0.014 1.50e-02 4.44e+03 9.18e-01
  bond pdb=" CB  THR A 335 "
       pdb=" CG2 THR A 335 "
    ideal  model  delta    sigma   weight residual
    1.521  1.492  0.029 3.30e-02 9.18e+02 7.70e-01
  bond pdb=" N   GLU A  40 "
       pdb=" CA  GLU A  40 "
    ideal  model  delta    sigma   weight residual
    1.457  1.468 -0.011 1.29e-02 6.01e+03 7.25e-01
  ... (remaining 15413 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.81: 27681
        1.81 -     3.63: 227
        3.63 -     5.44: 13
        5.44 -     7.25: 2
        7.25 -     9.07: 2
  Bond angle restraints: 27925
  Sorted by residual:
  angle pdb=" N   ILE A 245 "
        pdb=" CA  ILE A 245 "
        pdb=" C   ILE A 245 "
      ideal   model   delta    sigma   weight residual
     112.96  109.47    3.49 1.00e+00 1.00e+00 1.22e+01
  angle pdb=" O1P CMP A1401 "
        pdb=" P   CMP A1401 "
        pdb=" O2P CMP A1401 "
      ideal   model   delta    sigma   weight residual
     109.50  118.57   -9.07 3.00e+00 1.11e-01 9.14e+00
  angle pdb=" C5' CMP A1401 "
        pdb=" C4' CMP A1401 "
        pdb=" O4' CMP A1401 "
      ideal   model   delta    sigma   weight residual
     109.80  113.66   -3.86 1.50e+00 4.44e-01 6.64e+00
  angle pdb=" C3' CMP A1401 "
        pdb=" O3' CMP A1401 "
        pdb=" P   CMP A1401 "
      ideal   model   delta    sigma   weight residual
     120.50  112.83    7.67 3.00e+00 1.11e-01 6.53e+00
  angle pdb=" C2' CMP A1401 "
        pdb=" C3' CMP A1401 "
        pdb=" O3' CMP A1401 "
      ideal   model   delta    sigma   weight residual
     113.70  117.25   -3.55 1.50e+00 4.44e-01 5.61e+00
  ... (remaining 27920 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.48: 6942
       28.48 -    56.97: 213
       56.97 -    85.45: 16
       85.45 -   113.94: 2
      113.94 -   142.42: 2
  Dihedral angle restraints: 7175
    sinusoidal: 3879
      harmonic: 3296
  Sorted by residual:
  dihedral pdb=" C8  CMP A1401 "
           pdb=" C1' CMP A1401 "
           pdb=" N9  CMP A1401 "
           pdb=" O4' CMP A1401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -28.22 -170.65  142.42     1      2.00e+01 2.50e-03 4.30e+01
  dihedral pdb=" CA  ASP A 834 "
           pdb=" C   ASP A 834 "
           pdb=" N   LEU A 835 "
           pdb=" CA  LEU A 835 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.54  -17.46     0      5.00e+00 4.00e-02 1.22e+01
  dihedral pdb=" CA  CYS A1226 "
           pdb=" C   CYS A1226 "
           pdb=" N   THR A1227 "
           pdb=" CA  THR A1227 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.75   17.25     0      5.00e+00 4.00e-02 1.19e+01
  ... (remaining 7172 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 748
       0.029 -    0.059: 319
       0.059 -    0.088: 107
       0.088 -    0.117: 36
       0.117 -    0.146: 10
  Chirality restraints: 1220
  Sorted by residual:
  chirality pdb=" CA  VAL A 860 "
            pdb=" N   VAL A 860 "
            pdb=" C   VAL A 860 "
            pdb=" CB  VAL A 860 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.36e-01
  chirality pdb=" CA  ILE A 861 "
            pdb=" N   ILE A 861 "
            pdb=" C   ILE A 861 "
            pdb=" CB  ILE A 861 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.22e-01
  chirality pdb=" CG  LEU A 357 "
            pdb=" CB  LEU A 357 "
            pdb=" CD1 LEU A 357 "
            pdb=" CD2 LEU A 357 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.46   -0.13 2.00e-01 2.50e+01 4.19e-01
  ... (remaining 1217 not shown)

  Planarity restraints: 2185
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A  11 "   -0.019 5.00e-02 4.00e+02   2.92e-02 1.36e+00
        pdb=" N   PRO A  12 "    0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO A  12 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A  12 "   -0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 218 "   -0.017 5.00e-02 4.00e+02   2.55e-02 1.04e+00
        pdb=" N   PRO A 219 "    0.044 5.00e-02 4.00e+02
        pdb=" CA  PRO A 219 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A 219 "   -0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 799 "    0.005 2.00e-02 2.50e+03   9.69e-03 9.40e-01
        pdb=" C   ASN A 799 "   -0.017 2.00e-02 2.50e+03
        pdb=" O   ASN A 799 "    0.006 2.00e-02 2.50e+03
        pdb=" N   LYS A 800 "    0.006 2.00e-02 2.50e+03
  ... (remaining 2182 not shown)

  Histogram of nonbonded interaction distances:
        1.66 -     2.25: 1533
        2.25 -     2.84: 34305
        2.84 -     3.42: 35826
        3.42 -     4.01: 47527
        4.01 -     4.60: 75353
  Nonbonded interactions: 194544
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 181 "
            pdb="HH22 ARG A 915 "
     model   vdw
     1.659 2.450
  nonbonded pdb=" O   GLU A 803 "
            pdb=" HZ3 LYS A 807 "
     model   vdw
     1.686 2.450
  nonbonded pdb=" O   TYR A1016 "
            pdb=" HG1 THR A1017 "
     model   vdw
     1.702 2.450
  nonbonded pdb=" O   TYR A 768 "
            pdb=" HG1 THR A 772 "
     model   vdw
     1.705 2.450
  nonbonded pdb=" O   LEU A 940 "
            pdb=" HG1 THR A 944 "
     model   vdw
     1.710 2.450
  ... (remaining 194539 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:             1.090
  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:             0.090
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     14.020
  Find NCS groups from input model:        0.060
  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:6.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   7700  Z= 0.161
  Angle     :  0.574   9.068  10443  Z= 0.330
  Chirality :  0.038   0.146   1220
  Planarity :  0.003   0.029   1283
  Dihedral  : 12.972 142.422   2799
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 3.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -3.54 (0.24), residues: 925
  helix: -1.53 (0.19), residues: 636
  sheet: -3.27 (0.80), residues: 34
  loop : -4.04 (0.27), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 887 
 TYR   0.016   0.001   TYR A 768 
 PHE   0.012   0.001   PHE A 948 
 TRP   0.015   0.001   TRP A 763 
 HIS   0.004   0.001   HIS A  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 7700)
  covalent geometry    : angle       0.57381 (10443)
  hydrogen bonds       : bond        0.14452 (  406)
  hydrogen bonds       : angle       4.83218 ( 1188)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
REVERT: A   67 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7620 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 121
  average time/residue: 1.3072
  time to fit residues: 166.3462
Evaluate side-chains
  70 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    9.9990
   overall best weight:    0.9986

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

Flipped N/Q/H residues before XYZ refinement:
A 122 ASN
A1141 HIS
A1195 ASN
A1236 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.181664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.121827 restraints weight = 25969.792|
|-----------------------------------------------------------------------------|
r_work (start): 0.3559 rms_B_bonded: 2.53
r_work: 0.3441 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3312 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7299
moved from start:          0.2089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7700  Z= 0.151
  Angle     :  0.553   7.781  10443  Z= 0.293
  Chirality :  0.039   0.143   1220
  Planarity :  0.004   0.036   1283
  Dihedral  :  7.297 139.943   1018
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  :  9.95 %
    Favored  : 88.59 %
  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: -2.17 (0.27), residues: 925
  helix: -0.47 (0.21), residues: 641
  sheet: -2.82 (0.87), residues: 34
  loop : -3.63 (0.30), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 998 
 TYR   0.012   0.001   TYR A  92 
 PHE   0.015   0.001   PHE A 336 
 TRP   0.008   0.001   TRP A 763 
 HIS   0.003   0.001   HIS A 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 7700)
  covalent geometry    : angle       0.55316 (10443)
  hydrogen bonds       : bond        0.06414 (  406)
  hydrogen bonds       : angle       4.03671 ( 1188)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 GLU cc_start: 0.7465 (tm-30) cc_final: 0.6921 (tm-30)
REVERT: A  706 ARG cc_start: 0.6708 (OUTLIER) cc_final: 0.5916 (ttm170)
REVERT: A  721 ASN cc_start: 0.7653 (m-40) cc_final: 0.7355 (m110)
REVERT: A  803 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7225 (pm20)
REVERT: A  952 LEU cc_start: 0.6686 (OUTLIER) cc_final: 0.6407 (tt)
REVERT: A 1020 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7115 (mp0)
REVERT: A 1049 MET cc_start: 0.6061 (ptm) cc_final: 0.5445 (ptp)
REVERT: A 1086 SER cc_start: 0.8091 (m) cc_final: 0.7832 (p)
  outliers start: 12
  outliers final: 1
  residues processed: 84
  average time/residue: 1.0671
  time to fit residues: 95.3760
Evaluate side-chains
  68 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  706 ARG
Chi-restraints excluded: chain A residue  803 GLU
Chi-restraints excluded: chain A residue  823 ASN
Chi-restraints excluded: chain A residue  952 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 67 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 75 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 74 optimal weight:    6.9990
   chunk 65 optimal weight:    0.9980
   chunk 71 optimal weight:    7.9990
   overall best weight:    1.1986

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

Flipped N/Q/H residues before XYZ refinement:
A 122 ASN
A 387 GLN
A 994 GLN
A1236 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.177467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.116730 restraints weight = 26242.559|
|-----------------------------------------------------------------------------|
r_work (start): 0.3494 rms_B_bonded: 2.52
r_work: 0.3376 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3246 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7339
moved from start:          0.2647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7700  Z= 0.160
  Angle     :  0.554   7.263  10443  Z= 0.293
  Chirality :  0.038   0.144   1220
  Planarity :  0.003   0.042   1283
  Dihedral  :  7.328 141.189   1018
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 12.01 %
    Favored  : 86.17 %
  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: -1.56 (0.28), residues: 925
  helix: -0.10 (0.21), residues: 644
  sheet: -2.53 (0.89), residues: 34
  loop : -3.21 (0.34), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 998 
 TYR   0.015   0.001   TYR A  92 
 PHE   0.015   0.001   PHE A 352 
 TRP   0.009   0.001   TRP A 947 
 HIS   0.004   0.001   HIS A 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 7700)
  covalent geometry    : angle       0.55436 (10443)
  hydrogen bonds       : bond        0.06697 (  406)
  hydrogen bonds       : angle       3.99732 ( 1188)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 69
  time to evaluate  : 0.412 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 GLU cc_start: 0.7542 (tm-30) cc_final: 0.6984 (tm-30)
REVERT: A  803 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7280 (pm20)
REVERT: A 1049 MET cc_start: 0.6257 (ptm) cc_final: 0.5726 (ptp)
REVERT: A 1086 SER cc_start: 0.8291 (m) cc_final: 0.8039 (p)
  outliers start: 15
  outliers final: 1
  residues processed: 78
  average time/residue: 1.0718
  time to fit residues: 89.1449
Evaluate side-chains
  64 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 62
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  803 GLU
Chi-restraints excluded: chain A residue 1229 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 0 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 83 optimal weight:   10.0000
   chunk 90 optimal weight:    5.9990
   chunk 28 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 122 ASN
A1236 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.173298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.111627 restraints weight = 26333.339|
|-----------------------------------------------------------------------------|
r_work (start): 0.3406 rms_B_bonded: 2.56
r_work: 0.3287 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3162 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7383
moved from start:          0.3123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   7700  Z= 0.217
  Angle     :  0.594   6.936  10443  Z= 0.320
  Chirality :  0.040   0.151   1220
  Planarity :  0.004   0.047   1283
  Dihedral  :  7.454 142.896   1018
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.49 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 13.59 %
    Favored  : 84.83 %
  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: -1.56 (0.28), residues: 925
  helix: -0.10 (0.21), residues: 648
  sheet: -2.35 (0.89), residues: 34
  loop : -3.24 (0.33), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 998 
 TYR   0.015   0.002   TYR A 339 
 PHE   0.017   0.002   PHE A 336 
 TRP   0.010   0.001   TRP A 947 
 HIS   0.004   0.001   HIS A 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00525 ( 7700)
  covalent geometry    : angle       0.59437 (10443)
  hydrogen bonds       : bond        0.07511 (  406)
  hydrogen bonds       : angle       4.16891 ( 1188)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 70
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  278 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7551 (tm-30)
REVERT: A  803 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7330 (pm20)
REVERT: A 1049 MET cc_start: 0.6454 (ptm) cc_final: 0.5876 (ptp)
  outliers start: 13
  outliers final: 3
  residues processed: 79
  average time/residue: 1.1191
  time to fit residues: 94.0082
Evaluate side-chains
  69 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 64
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ASP
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  803 GLU
Chi-restraints excluded: chain A residue 1198 LEU
Chi-restraints excluded: chain A residue 1229 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 53 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   chunk 76 optimal weight:    5.9990
   chunk 29 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 122 ASN
A1236 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.175860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.116865 restraints weight = 26351.770|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 2.73
r_work: 0.3333 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3205 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7386
moved from start:          0.3214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7700  Z= 0.134
  Angle     :  0.533   7.025  10443  Z= 0.283
  Chirality :  0.037   0.139   1220
  Planarity :  0.003   0.045   1283
  Dihedral  :  7.376 140.982   1018
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 13.96 %
    Favored  : 84.47 %
  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: -1.15 (0.28), residues: 925
  helix:  0.19 (0.21), residues: 645
  sheet: -2.23 (0.90), residues: 34
  loop : -3.03 (0.35), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A1090 
 TYR   0.010   0.001   TYR A 339 
 PHE   0.013   0.001   PHE A 352 
 TRP   0.008   0.001   TRP A 733 
 HIS   0.004   0.001   HIS A 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 7700)
  covalent geometry    : angle       0.53297 (10443)
  hydrogen bonds       : bond        0.06504 (  406)
  hydrogen bonds       : angle       3.94758 ( 1188)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 71
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LEU cc_start: 0.6660 (OUTLIER) cc_final: 0.6406 (pp)
REVERT: A  278 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7509 (tm-30)
REVERT: A  803 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7298 (pm20)
REVERT: A 1020 GLU cc_start: 0.7930 (mm-30) cc_final: 0.6945 (mp0)
  outliers start: 13
  outliers final: 2
  residues processed: 79
  average time/residue: 1.0433
  time to fit residues: 87.9954
Evaluate side-chains
  69 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 64
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  803 GLU
Chi-restraints excluded: chain A residue 1198 LEU
Chi-restraints excluded: chain A residue 1229 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 67 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 56 optimal weight:    1.9990
   chunk 80 optimal weight:    5.9990
   chunk 90 optimal weight:    5.9990
   chunk 71 optimal weight:    8.9990
   chunk 92 optimal weight:    3.9990
   chunk 78 optimal weight:    0.6980
   chunk 39 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 33 optimal weight:    0.5980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 122 ASN
A1236 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.176102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.115392 restraints weight = 26245.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.3458 rms_B_bonded: 2.50
r_work: 0.3345 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3218 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7365
moved from start:          0.3348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7700  Z= 0.131
  Angle     :  0.527   7.288  10443  Z= 0.278
  Chirality :  0.037   0.139   1220
  Planarity :  0.003   0.043   1283
  Dihedral  :  7.267 139.108   1018
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 14.81 %
    Favored  : 83.62 %
  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: -0.91 (0.28), residues: 925
  helix:  0.36 (0.22), residues: 646
  sheet: -2.12 (0.93), residues: 34
  loop : -2.93 (0.34), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1132 
 TYR   0.009   0.001   TYR A 339 
 PHE   0.015   0.001   PHE A 324 
 TRP   0.008   0.001   TRP A 733 
 HIS   0.003   0.001   HIS A 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 7700)
  covalent geometry    : angle       0.52717 (10443)
  hydrogen bonds       : bond        0.06135 (  406)
  hydrogen bonds       : angle       3.83865 ( 1188)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LEU cc_start: 0.6642 (OUTLIER) cc_final: 0.6381 (pp)
REVERT: A  278 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7560 (tm-30)
REVERT: A  706 ARG cc_start: 0.7119 (OUTLIER) cc_final: 0.6080 (ttm170)
REVERT: A  803 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7304 (pm20)
  outliers start: 13
  outliers final: 3
  residues processed: 76
  average time/residue: 1.1239
  time to fit residues: 91.2530
Evaluate side-chains
  73 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  706 ARG
Chi-restraints excluded: chain A residue  736 SER
Chi-restraints excluded: chain A residue  803 GLU
Chi-restraints excluded: chain A residue 1198 LEU
Chi-restraints excluded: chain A residue 1229 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 71 optimal weight:    7.9990
   chunk 43 optimal weight:    0.9980
   chunk 72 optimal weight:    6.9990
   chunk 24 optimal weight:    0.0980
   chunk 34 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 60 optimal weight:    5.9990
   chunk 3 optimal weight:    3.9990
   chunk 0 optimal weight:    0.9980
   chunk 90 optimal weight:    5.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
A1236 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.173984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.112785 restraints weight = 26201.806|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 2.53
r_work: 0.3306 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3178 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7358
moved from start:          0.3511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7700  Z= 0.160
  Angle     :  0.547   6.997  10443  Z= 0.291
  Chirality :  0.038   0.145   1220
  Planarity :  0.003   0.043   1283
  Dihedral  :  7.313 139.881   1018
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 15.53 %
    Favored  : 83.01 %
  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: -0.90 (0.28), residues: 925
  helix:  0.35 (0.21), residues: 647
  sheet: -1.98 (0.96), residues: 34
  loop : -2.88 (0.35), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 165 
 TYR   0.012   0.001   TYR A 339 
 PHE   0.015   0.001   PHE A 352 
 TRP   0.008   0.001   TRP A 947 
 HIS   0.004   0.001   HIS A 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 7700)
  covalent geometry    : angle       0.54699 (10443)
  hydrogen bonds       : bond        0.06637 (  406)
  hydrogen bonds       : angle       3.91796 ( 1188)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 67
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LEU cc_start: 0.6693 (OUTLIER) cc_final: 0.6448 (pp)
REVERT: A  278 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7529 (tm-30)
REVERT: A  706 ARG cc_start: 0.7093 (OUTLIER) cc_final: 0.6058 (ttm170)
REVERT: A  803 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7319 (pm20)
REVERT: A 1049 MET cc_start: 0.6646 (ptm) cc_final: 0.6042 (ptp)
  outliers start: 12
  outliers final: 3
  residues processed: 73
  average time/residue: 1.0559
  time to fit residues: 82.2925
Evaluate side-chains
  71 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 64
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  706 ARG
Chi-restraints excluded: chain A residue  736 SER
Chi-restraints excluded: chain A residue  803 GLU
Chi-restraints excluded: chain A residue 1198 LEU
Chi-restraints excluded: chain A residue 1229 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 87 optimal weight:    8.9990
   chunk 14 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9980
   chunk 12 optimal weight:    0.5980
   chunk 7 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   chunk 74 optimal weight:   10.0000
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
A1236 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.174065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.113083 restraints weight = 26445.252|
|-----------------------------------------------------------------------------|
r_work (start): 0.3427 rms_B_bonded: 2.51
r_work: 0.3302 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3177 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7329
moved from start:          0.3625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7700  Z= 0.151
  Angle     :  0.544   7.087  10443  Z= 0.289
  Chirality :  0.038   0.143   1220
  Planarity :  0.003   0.043   1283
  Dihedral  :  7.282 139.250   1018
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 16.02 %
    Favored  : 82.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.79 (0.29), residues: 925
  helix:  0.42 (0.21), residues: 647
  sheet: -1.82 (1.00), residues: 34
  loop : -2.81 (0.35), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 165 
 TYR   0.011   0.001   TYR A 339 
 PHE   0.014   0.001   PHE A 352 
 TRP   0.008   0.001   TRP A 733 
 HIS   0.003   0.001   HIS A 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 7700)
  covalent geometry    : angle       0.54450 (10443)
  hydrogen bonds       : bond        0.06498 (  406)
  hydrogen bonds       : angle       3.87687 ( 1188)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LEU cc_start: 0.6702 (OUTLIER) cc_final: 0.6466 (pp)
REVERT: A  706 ARG cc_start: 0.7103 (OUTLIER) cc_final: 0.5742 (tpm170)
REVERT: A  803 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7299 (pm20)
REVERT: A 1049 MET cc_start: 0.6727 (ptm) cc_final: 0.6095 (ptp)
  outliers start: 9
  outliers final: 3
  residues processed: 71
  average time/residue: 1.0181
  time to fit residues: 77.1259
Evaluate side-chains
  73 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 67
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  706 ARG
Chi-restraints excluded: chain A residue  736 SER
Chi-restraints excluded: chain A residue  803 GLU
Chi-restraints excluded: chain A residue 1198 LEU
Chi-restraints excluded: chain A residue 1229 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   chunk 68 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 84 optimal weight:    8.9990
   chunk 71 optimal weight:    4.9990
   chunk 23 optimal weight:    0.8980
   chunk 36 optimal weight:    0.6980
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
A1236 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.174136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.121361 restraints weight = 26345.804|
|-----------------------------------------------------------------------------|
r_work (start): 0.3521 rms_B_bonded: 2.58
r_work: 0.3287 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3161 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.3715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7700  Z= 0.151
  Angle     :  0.546   7.044  10443  Z= 0.290
  Chirality :  0.038   0.142   1220
  Planarity :  0.003   0.042   1283
  Dihedral  :  7.276 138.964   1018
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 15.90 %
    Favored  : 82.65 %
  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: -0.75 (0.29), residues: 925
  helix:  0.44 (0.21), residues: 647
  sheet: -1.82 (1.00), residues: 34
  loop : -2.75 (0.35), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 887 
 TYR   0.011   0.001   TYR A 339 
 PHE   0.014   0.001   PHE A 352 
 TRP   0.008   0.001   TRP A 733 
 HIS   0.003   0.001   HIS A 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 7700)
  covalent geometry    : angle       0.54611 (10443)
  hydrogen bonds       : bond        0.06506 (  406)
  hydrogen bonds       : angle       3.87914 ( 1188)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 67
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LEU cc_start: 0.6948 (OUTLIER) cc_final: 0.6681 (pp)
REVERT: A  706 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.5991 (tpm170)
REVERT: A  803 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7544 (pm20)
REVERT: A 1020 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7025 (mp0)
REVERT: A 1049 MET cc_start: 0.6925 (ptm) cc_final: 0.6338 (ptp)
  outliers start: 12
  outliers final: 4
  residues processed: 74
  average time/residue: 0.9366
  time to fit residues: 74.0450
Evaluate side-chains
  73 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  706 ARG
Chi-restraints excluded: chain A residue  736 SER
Chi-restraints excluded: chain A residue  803 GLU
Chi-restraints excluded: chain A residue 1002 GLU
Chi-restraints excluded: chain A residue 1198 LEU
Chi-restraints excluded: chain A residue 1229 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 50 optimal weight:    0.9980
   chunk 82 optimal weight:   10.0000
   chunk 20 optimal weight:    1.9990
   chunk 59 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   chunk 73 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9990
   chunk 80 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.9786

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

Flipped N/Q/H residues before XYZ refinement:
A1236 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.174571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.121859 restraints weight = 26537.672|
|-----------------------------------------------------------------------------|
r_work (start): 0.3526 rms_B_bonded: 2.58
r_work: 0.3276 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3145 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.3767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7700  Z= 0.143
  Angle     :  0.544   7.126  10443  Z= 0.289
  Chirality :  0.038   0.140   1220
  Planarity :  0.003   0.042   1283
  Dihedral  :  7.269 138.494   1018
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 16.14 %
    Favored  : 82.77 %
  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: -0.67 (0.29), residues: 925
  helix:  0.49 (0.22), residues: 647
  sheet: -1.83 (1.01), residues: 34
  loop : -2.70 (0.36), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 165 
 TYR   0.010   0.001   TYR A 339 
 PHE   0.019   0.001   PHE A 324 
 TRP   0.008   0.001   TRP A 733 
 HIS   0.003   0.001   HIS A 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 7700)
  covalent geometry    : angle       0.54355 (10443)
  hydrogen bonds       : bond        0.06356 (  406)
  hydrogen bonds       : angle       3.84276 ( 1188)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LEU cc_start: 0.6867 (OUTLIER) cc_final: 0.6607 (pp)
REVERT: A  706 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.5932 (tpm170)
REVERT: A  803 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7502 (pm20)
REVERT: A 1004 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7187 (mt-10)
REVERT: A 1049 MET cc_start: 0.6937 (ptm) cc_final: 0.6381 (ptp)
  outliers start: 9
  outliers final: 4
  residues processed: 71
  average time/residue: 1.0153
  time to fit residues: 76.9116
Evaluate side-chains
  73 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  706 ARG
Chi-restraints excluded: chain A residue  736 SER
Chi-restraints excluded: chain A residue  803 GLU
Chi-restraints excluded: chain A residue 1002 GLU
Chi-restraints excluded: chain A residue 1198 LEU
Chi-restraints excluded: chain A residue 1229 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 36 optimal weight:    0.5980
   chunk 86 optimal weight:    4.9990
   chunk 81 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9990
   chunk 10 optimal weight:    0.0570
   chunk 56 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 59 optimal weight:    4.9990
   chunk 78 optimal weight:    3.9990
   overall best weight:    0.6500

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

Flipped N/Q/H residues before XYZ refinement:
A 122 ASN
A1236 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.176242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.123817 restraints weight = 26303.551|
|-----------------------------------------------------------------------------|
r_work (start): 0.3548 rms_B_bonded: 2.50
r_work: 0.3310 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3179 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.3783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7700  Z= 0.121
  Angle     :  0.522   7.303  10443  Z= 0.276
  Chirality :  0.037   0.133   1220
  Planarity :  0.003   0.042   1283
  Dihedral  :  7.166 136.205   1018
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 16.14 %
    Favored  : 82.65 %
  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 (0.29), residues: 925
  helix:  0.67 (0.22), residues: 648
  sheet: -1.89 (0.98), residues: 34
  loop : -2.62 (0.36), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 998 
 TYR   0.008   0.001   TYR A 339 
 PHE   0.011   0.001   PHE A 352 
 TRP   0.008   0.001   TRP A 763 
 HIS   0.003   0.001   HIS A 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 7700)
  covalent geometry    : angle       0.52194 (10443)
  hydrogen bonds       : bond        0.05734 (  406)
  hydrogen bonds       : angle       3.70378 ( 1188)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5161.82 seconds
wall clock time: 87 minutes 51.78 seconds (5271.78 seconds total)