Starting phenix.real_space_refine
on Wed Sep 17 14:08:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kg2_62306/09_2025/9kg2_62306.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kg2_62306/09_2025/9kg2_62306.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kg2_62306/09_2025/9kg2_62306.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kg2_62306/09_2025/9kg2_62306.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kg2_62306/09_2025/9kg2_62306.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kg2_62306/09_2025/9kg2_62306.map"
  }
  resolution = 4.1
  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=   0.049
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      37      5.16       5
     C    5752      2.51       5
     N    1518      2.21       5
     O    1657      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8964
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 8964
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1166, 8964
          Classifications: {'peptide': 1166}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 29, 'TRANS': 1136}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
  Time building chain proxies: 2.33, per 1000 atoms: 0.26
  Number of scatterers: 8964
  At special positions: 0
  Unit cell: (74.106, 112.77, 146.064, 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      37     16.00
     O    1657      8.00
     N    1518      7.00
     C    5752      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.98
  Conformation dependent library (CDL) restraints added in 410.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2132

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 6 sheets defined
      62.0% alpha, 3.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.49
  Creating SS restraints...
    Processing helix  chain 'A' and resid 37 through 55
    Processing helix  chain 'A' and resid 56 through 72
      removed outlier: 3.667A  pdb=" N   LEU A  60 " --> pdb=" O   PRO A  56 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   ASN A  72 " --> pdb=" O   GLY A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 128
      removed outlier: 4.342A  pdb=" N   ARG A  85 " --> pdb=" O   HIS A  81 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   TYR A  86 " --> pdb=" O   GLU A  82 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   LEU A 128 " --> pdb=" O   LEU A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 135
      removed outlier: 4.028A  pdb=" N   PHE A 134 " --> pdb=" O   ASP A 131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 182
      removed outlier: 3.791A  pdb=" N   VAL A 145 " --> pdb=" O   THR A 141 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   PHE A 146 " --> pdb=" O   GLY A 142 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   ASP A 151 " --> pdb=" O   SER A 147 " (cutoff:3.500A)
      removed outlier: 5.202A  pdb=" N   GLY A 164 " --> pdb=" O   SER A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 194
      removed outlier: 3.861A  pdb=" N   LEU A 190 " --> pdb=" O   LYS A 186 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   VAL A 194 " --> pdb=" O   LEU A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 217
      removed outlier: 3.509A  pdb=" N   ALA A 201 " --> pdb=" O   GLY A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 233
      removed outlier: 3.754A  pdb=" N   ASN A 222 " --> pdb=" O   GLU A 218 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   ALA A 223 " --> pdb=" O   SER A 219 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   ILE A 226 " --> pdb=" O   ASN A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 238
    Processing helix  chain 'A' and resid 244 through 295
      removed outlier: 3.617A  pdb=" N   TYR A 256 " --> pdb=" O   ASP A 252 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ARG A 295 " --> pdb=" O   GLY A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 301 through 317
    Processing helix  chain 'A' and resid 321 through 323
      No H-bonds generated for 'chain 'A' and resid 321 through 323'
    Processing helix  chain 'A' and resid 324 through 336
      removed outlier: 3.921A  pdb=" N   PHE A 328 " --> pdb=" O   ASN A 324 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   SER A 329 " --> pdb=" O   LEU A 325 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   LYS A 330 " --> pdb=" O   GLY A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 415
      removed outlier: 3.695A  pdb=" N   SER A 411 " --> pdb=" O   SER A 407 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   ILE A 413 " --> pdb=" O   VAL A 409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 435 through 441
      removed outlier: 3.958A  pdb=" N   LEU A 439 " --> pdb=" O   GLN A 435 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   GLU A 441 " --> pdb=" O   LYS A 437 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 456 through 463
    Processing helix  chain 'A' and resid 469 through 480
    Processing helix  chain 'A' and resid 499 through 503
    Processing helix  chain 'A' and resid 511 through 521
      removed outlier: 4.344A  pdb=" N   ALA A 515 " --> pdb=" O   ARG A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 529 through 533
      removed outlier: 3.757A  pdb=" N   ALA A 533 " --> pdb=" O   ALA A 530 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 536 through 549
    Processing helix  chain 'A' and resid 584 through 589
      removed outlier: 3.777A  pdb=" N   ILE A 589 " --> pdb=" O   HIS A 585 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 590 through 593
    Processing helix  chain 'A' and resid 595 through 605
    Processing helix  chain 'A' and resid 675 through 680
    Processing helix  chain 'A' and resid 687 through 698
    Processing helix  chain 'A' and resid 699 through 715
      removed outlier: 3.563A  pdb=" N   THR A 703 " --> pdb=" O   PHE A 699 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   PHE A 715 " --> pdb=" O   MET A 711 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 722 through 773
      removed outlier: 3.855A  pdb=" N   LYS A 726 " --> pdb=" O   SER A 722 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   VAL A 742 " --> pdb=" O   GLY A 738 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   LEU A 746 " --> pdb=" O   VAL A 742 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   ILE A 747 " --> pdb=" O   GLY A 743 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   SER A 753 " --> pdb=" O   HIS A 749 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   ILE A 754 " --> pdb=" O   TYR A 750 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   MET A 755 " --> pdb=" O   PHE A 751 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   LEU A 759 " --> pdb=" O   MET A 755 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   THR A 760 " --> pdb=" O   GLY A 756 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   ARG A 765 " --> pdb=" O   THR A 761 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   MET A 766 " --> pdb=" O   ARG A 762 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 775 through 780
    Processing helix  chain 'A' and resid 785 through 805
      removed outlier: 4.120A  pdb=" N   ALA A 790 " --> pdb=" O   SER A 786 " (cutoff:3.500A)
      removed outlier: 4.400A  pdb=" N   ALA A 791 " --> pdb=" O   SER A 787 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ALA A 798 " --> pdb=" O   ALA A 794 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   VAL A 800 " --> pdb=" O   ASP A 796 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   LYS A 801 " --> pdb=" O   ALA A 797 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   SER A 802 " --> pdb=" O   ALA A 798 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 805 through 829
      removed outlier: 3.566A  pdb=" N   SER A 809 " --> pdb=" O   ALA A 805 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 832 through 856
      removed outlier: 3.771A  pdb=" N   ILE A 836 " --> pdb=" O   VAL A 832 " (cutoff:3.500A)
      Proline residue:  A 841  - end of helix
      removed outlier: 4.021A  pdb=" N   LEU A 854 " --> pdb=" O   GLN A 850 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   LYS A 855 " --> pdb=" O   GLN A 851 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   GLY A 856 " --> pdb=" O   LEU A 852 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 865 through 876
      removed outlier: 4.216A  pdb=" N   SER A 869 " --> pdb=" O   HIS A 865 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ILE A 871 " --> pdb=" O   LYS A 867 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 878 through 884
    Processing helix  chain 'A' and resid 887 through 899
      removed outlier: 3.503A  pdb=" N   LEU A 899 " --> pdb=" O   PHE A 895 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 899 through 939
      removed outlier: 3.627A  pdb=" N   GLN A 903 " --> pdb=" O   LEU A 899 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   GLN A 911 " --> pdb=" O   LEU A 907 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   LEU A 916 " --> pdb=" O   THR A 912 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ALA A 923 " --> pdb=" O   LEU A 919 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   LEU A 924 " --> pdb=" O   SER A 920 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   TYR A 925 " --> pdb=" O   GLN A 921 " (cutoff:3.500A)
      removed outlier: 4.345A  pdb=" N   GLU A 928 " --> pdb=" O   LEU A 924 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ALA A 929 " --> pdb=" O   TYR A 925 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 953 through 963
      removed outlier: 3.540A  pdb=" N   ILE A 958 " --> pdb=" O   VAL A 954 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   THR A 959 " --> pdb=" O   VAL A 955 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 963 through 969
      removed outlier: 3.869A  pdb=" N   VAL A 967 " --> pdb=" O   VAL A 963 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 969 through 974
      removed outlier: 3.802A  pdb=" N   ILE A 973 " --> pdb=" O   LEU A 969 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1051 through 1059
      removed outlier: 4.221A  pdb=" N   ILE A1055 " --> pdb=" O   LYS A1051 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   ALA A1056 " --> pdb=" O   SER A1052 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ILE A1058 " --> pdb=" O   VAL A1054 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   GLU A1059 " --> pdb=" O   ILE A1055 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1077 through 1079
      No H-bonds generated for 'chain 'A' and resid 1077 through 1079'
    Processing helix  chain 'A' and resid 1080 through 1087
    Processing helix  chain 'A' and resid 1101 through 1108
    Processing helix  chain 'A' and resid 1114 through 1126
    Processing helix  chain 'A' and resid 1127 through 1133
      removed outlier: 3.584A  pdb=" N   GLY A1133 " --> pdb=" O   GLY A1129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1136 through 1140
      removed outlier: 3.536A  pdb=" N   THR A1140 " --> pdb=" O   GLY A1137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1152 through 1166
    Processing helix  chain 'A' and resid 1183 through 1195
      removed outlier: 3.839A  pdb=" N   LEU A1187 " --> pdb=" O   SER A1183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1229 through 1234
      removed outlier: 3.740A  pdb=" N   VAL A1234 " --> pdb=" O   HIS A1230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1239 through 1245
      removed outlier: 4.079A  pdb=" N   ARG A1243 " --> pdb=" O   GLY A1239 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 389 through 390
      removed outlier: 3.615A  pdb=" N   ILE A 365 " --> pdb=" O   PHE A 390 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 396 through 399
      removed outlier: 3.658A  pdb=" N   VAL A 399 " --> pdb=" O   ALA A 572 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   GLU A 581 " --> pdb=" O   VAL A 573 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1028 through 1034
      removed outlier: 6.739A  pdb=" N   ARG A1029 " --> pdb=" O   ASP A1016 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   ASP A1016 " --> pdb=" O   ARG A1029 " (cutoff:3.500A)
      removed outlier: 4.513A  pdb=" N   PHE A1031 " --> pdb=" O   HIS A1014 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   VAL A1015 " --> pdb=" O   ALA A1066 " (cutoff:3.500A)
      removed outlier: 6.105A  pdb=" N   ALA A1066 " --> pdb=" O   VAL A1015 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1041 through 1043
      removed outlier: 6.495A  pdb=" N   GLN A1041 " --> pdb=" O   VAL A1202 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1088 through 1089
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1219 through 1220
      removed outlier: 3.510A  pdb=" N   GLN A1220 " --> pdb=" O   ARG A1223 " (cutoff:3.500A)

    475 hydrogen bonds defined for protein.
    1386 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: 1.53

  Time building geometry restraints manager: 1.25 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2921
        1.34 -     1.46: 2124
        1.46 -     1.58: 4023
        1.58 -     1.70: 0
        1.70 -     1.82: 65
  Bond restraints: 9133
  Sorted by residual:
  bond pdb=" N   GLN A1248 "
       pdb=" CA  GLN A1248 "
    ideal  model  delta    sigma   weight residual
    1.457  1.480 -0.022 1.29e-02 6.01e+03 2.94e+00
  bond pdb=" CA  ASP A 521 "
       pdb=" CB  ASP A 521 "
    ideal  model  delta    sigma   weight residual
    1.522  1.530 -0.008 7.00e-03 2.04e+04 1.35e+00
  bond pdb=" N   VAL A 182 "
       pdb=" CA  VAL A 182 "
    ideal  model  delta    sigma   weight residual
    1.474  1.458  0.017 1.57e-02 4.06e+03 1.11e+00
  bond pdb=" CA  ASP A 521 "
       pdb=" C   ASP A 521 "
    ideal  model  delta    sigma   weight residual
    1.531  1.524  0.007 7.40e-03 1.83e+04 8.82e-01
  bond pdb=" N   ASP A1030 "
       pdb=" CA  ASP A1030 "
    ideal  model  delta    sigma   weight residual
    1.457  1.468 -0.011 1.29e-02 6.01e+03 7.29e-01
  ... (remaining 9128 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.96: 12158
        1.96 -     3.91: 163
        3.91 -     5.87: 31
        5.87 -     7.83: 2
        7.83 -     9.78: 4
  Bond angle restraints: 12358
  Sorted by residual:
  angle pdb=" C   PHE A 181 "
        pdb=" N   VAL A 182 "
        pdb=" CA  VAL A 182 "
      ideal   model   delta    sigma   weight residual
     121.65  116.70    4.95 9.40e-01 1.13e+00 2.77e+01
  angle pdb=" C   LEU A1247 "
        pdb=" N   GLN A1248 "
        pdb=" CA  GLN A1248 "
      ideal   model   delta    sigma   weight residual
     121.54  131.32   -9.78 1.91e+00 2.74e-01 2.62e+01
  angle pdb=" N   ILE A1131 "
        pdb=" CA  ILE A1131 "
        pdb=" C   ILE A1131 "
      ideal   model   delta    sigma   weight residual
     113.53  110.26    3.27 9.80e-01 1.04e+00 1.11e+01
  angle pdb=" C   SER A 160 "
        pdb=" N   GLU A 161 "
        pdb=" CA  GLU A 161 "
      ideal   model   delta    sigma   weight residual
     122.79  117.45    5.34 1.70e+00 3.46e-01 9.86e+00
  angle pdb=" CB  MET A 870 "
        pdb=" CG  MET A 870 "
        pdb=" SD  MET A 870 "
      ideal   model   delta    sigma   weight residual
     112.70  121.15   -8.45 3.00e+00 1.11e-01 7.94e+00
  ... (remaining 12353 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 4838
       17.98 -    35.96: 459
       35.96 -    53.94: 91
       53.94 -    71.92: 15
       71.92 -    89.90: 11
  Dihedral angle restraints: 5414
    sinusoidal: 2075
      harmonic: 3339
  Sorted by residual:
  dihedral pdb=" CA  LEU A1247 "
           pdb=" C   LEU A1247 "
           pdb=" N   GLN A1248 "
           pdb=" CA  GLN A1248 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.83   24.17     0      5.00e+00 4.00e-02 2.34e+01
  dihedral pdb=" CA  THR A1249 "
           pdb=" C   THR A1249 "
           pdb=" N   HIS A1250 "
           pdb=" CA  HIS A1250 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.47  -21.53     0      5.00e+00 4.00e-02 1.85e+01
  dihedral pdb=" CA  GLU A 441 "
           pdb=" C   GLU A 441 "
           pdb=" N   GLN A 442 "
           pdb=" CA  GLN A 442 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.40   19.60     0      5.00e+00 4.00e-02 1.54e+01
  ... (remaining 5411 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 839
       0.028 -    0.056: 341
       0.056 -    0.083: 160
       0.083 -    0.111: 64
       0.111 -    0.139: 19
  Chirality restraints: 1423
  Sorted by residual:
  chirality pdb=" CA  ILE A 349 "
            pdb=" N   ILE A 349 "
            pdb=" C   ILE A 349 "
            pdb=" CB  ILE A 349 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.83e-01
  chirality pdb=" CA  PHE A 309 "
            pdb=" N   PHE A 309 "
            pdb=" C   PHE A 309 "
            pdb=" CB  PHE A 309 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.81e-01
  chirality pdb=" CA  GLU A 441 "
            pdb=" N   GLU A 441 "
            pdb=" C   GLU A 441 "
            pdb=" CB  GLU A 441 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.10e-01
  ... (remaining 1420 not shown)

  Planarity restraints: 1574
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 159 "    0.010 2.00e-02 2.50e+03   1.90e-02 3.61e+00
        pdb=" C   ILE A 159 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   ILE A 159 "    0.012 2.00e-02 2.50e+03
        pdb=" N   SER A 160 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 157 "   -0.007 2.00e-02 2.50e+03   1.42e-02 2.01e+00
        pdb=" C   ASP A 157 "    0.025 2.00e-02 2.50e+03
        pdb=" O   ASP A 157 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   ALA A 158 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 681 "    0.022 5.00e-02 4.00e+02   3.26e-02 1.70e+00
        pdb=" N   PRO A 682 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A 682 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 682 "    0.018 5.00e-02 4.00e+02
  ... (remaining 1571 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1139
        2.75 -     3.29: 9686
        3.29 -     3.82: 14638
        3.82 -     4.36: 15990
        4.36 -     4.90: 26357
  Nonbonded interactions: 67810
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 529 "
            pdb=" OG  SER A 532 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" O   HIS A1128 "
            pdb=" OG  SER A1132 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" O   ARG A1029 "
            pdb=" NH2 ARG A1223 "
     model   vdw
     2.251 3.120
  nonbonded pdb=" O   GLY A 444 "
            pdb=" N   LEU A 526 "
     model   vdw
     2.298 3.120
  nonbonded pdb=" O   PHE A 438 "
            pdb=" NE2 GLN A 442 "
     model   vdw
     2.299 3.120
  ... (remaining 67805 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             1.180
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.670
  Find NCS groups from input model:        0.040
  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:1.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
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      :  0.003   0.025   9133  Z= 0.136
  Angle     :  0.605   9.781  12358  Z= 0.343
  Chirality :  0.041   0.139   1423
  Planarity :  0.003   0.033   1574
  Dihedral  : 14.828  89.902   3282
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.20 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  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 aren not related in a simple way.
  whole:  0.32 (0.26), residues: 1162
  helix:  1.47 (0.21), residues: 643
  sheet: -0.75 (0.89), residues: 39
  loop : -1.51 (0.28), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A1022 
 TYR   0.017   0.001   TYR A 205 
 PHE   0.020   0.001   PHE A 309 
 TRP   0.005   0.001   TRP A 283 
 HIS   0.002   0.001   HIS A 749 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 9133)
  covalent geometry    : angle       0.60511 (12358)
  hydrogen bonds       : bond        0.15124 (  475)
  hydrogen bonds       : angle       5.71207 ( 1386)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.343 
Fit side-chains
REVERT: A   75 ASP cc_start: 0.7706 (t0) cc_final: 0.7381 (t0)
REVERT: A 1016 ASP cc_start: 0.8810 (m-30) cc_final: 0.8555 (m-30)
REVERT: A 1057 MET cc_start: 0.8361 (tpp) cc_final: 0.7509 (tpp)
REVERT: A 1070 MET cc_start: 0.8527 (tmm) cc_final: 0.8287 (tmm)
REVERT: A 1090 LEU cc_start: 0.9458 (tp) cc_final: 0.9054 (tp)
REVERT: A 1119 ILE cc_start: 0.9234 (mm) cc_final: 0.8879 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.0798
  time to fit residues: 16.8162
Evaluate side-chains
  104 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 108 optimal weight:    7.9990
   chunk 49 optimal weight:    0.0980
   chunk 97 optimal weight:    2.9990
   chunk 113 optimal weight:    9.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    0.3980
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
A 115 GLN
A 442 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.160597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.114700 restraints weight = 19507.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.114357 restraints weight = 9627.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.115269 restraints weight = 7222.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.115664 restraints weight = 6296.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.115859 restraints weight = 5701.461|
|-----------------------------------------------------------------------------|
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.0846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9133  Z= 0.157
  Angle     :  0.582  10.181  12358  Z= 0.311
  Chirality :  0.041   0.144   1423
  Planarity :  0.004   0.036   1574
  Dihedral  :  4.251  21.556   1266
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.37 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  6.43 %
    Favored  : 93.47 %
  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 aren not related in a simple way.
  whole:  0.37 (0.26), residues: 1162
  helix:  1.49 (0.21), residues: 662
  sheet: -0.76 (0.90), residues: 39
  loop : -1.56 (0.29), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1223 
 TYR   0.012   0.001   TYR A  86 
 PHE   0.012   0.001   PHE A 287 
 TRP   0.004   0.001   TRP A 933 
 HIS   0.005   0.001   HIS A1128 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 9133)
  covalent geometry    : angle       0.58203 (12358)
  hydrogen bonds       : bond        0.05992 (  475)
  hydrogen bonds       : angle       4.80742 ( 1386)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 140
  time to evaluate  : 0.355 
Fit side-chains
REVERT: A   75 ASP cc_start: 0.7677 (t0) cc_final: 0.7239 (t0)
REVERT: A  205 TYR cc_start: 0.8759 (t80) cc_final: 0.8499 (t80)
REVERT: A  266 MET cc_start: 0.8340 (tmm) cc_final: 0.7896 (tmm)
REVERT: A  711 MET cc_start: 0.7828 (ttt) cc_final: 0.7586 (ttm)
REVERT: A 1016 ASP cc_start: 0.8781 (m-30) cc_final: 0.8489 (m-30)
REVERT: A 1090 LEU cc_start: 0.9468 (tp) cc_final: 0.9083 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 141
  average time/residue: 0.0731
  time to fit residues: 15.9054
Evaluate side-chains
  112 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 107 optimal weight:    2.9990
   chunk 108 optimal weight:    9.9990
   chunk 71 optimal weight:    6.9990
   chunk 31 optimal weight:    0.5980
   chunk 21 optimal weight:    0.7980
   chunk 58 optimal weight:   10.0000
   chunk 24 optimal weight:    8.9990
   chunk 74 optimal weight:    0.9980
   chunk 46 optimal weight:    6.9990
   chunk 96 optimal weight:   10.0000
   overall best weight:    1.4784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.161311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.115892 restraints weight = 19469.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.117208 restraints weight = 10678.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.117448 restraints weight = 6946.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.117803 restraints weight = 5896.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.118003 restraints weight = 5429.166|
|-----------------------------------------------------------------------------|
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.1218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9133  Z= 0.143
  Angle     :  0.570  10.346  12358  Z= 0.301
  Chirality :  0.041   0.153   1423
  Planarity :  0.003   0.037   1574
  Dihedral  :  4.240  21.431   1266
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.45 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  6.11 %
    Favored  : 93.78 %
  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 aren not related in a simple way.
  whole:  0.37 (0.26), residues: 1162
  helix:  1.50 (0.21), residues: 664
  sheet: -0.75 (0.89), residues: 39
  loop : -1.60 (0.29), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1223 
 TYR   0.019   0.001   TYR A 276 
 PHE   0.019   0.001   PHE A 984 
 TRP   0.003   0.001   TRP A 684 
 HIS   0.003   0.001   HIS A 749 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 9133)
  covalent geometry    : angle       0.56968 (12358)
  hydrogen bonds       : bond        0.05751 (  475)
  hydrogen bonds       : angle       4.58205 ( 1386)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 148
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 ASP cc_start: 0.7551 (t0) cc_final: 0.7130 (t0)
REVERT: A  131 ASP cc_start: 0.8446 (t70) cc_final: 0.7952 (t70)
REVERT: A  266 MET cc_start: 0.8348 (tmm) cc_final: 0.7863 (tmm)
REVERT: A  438 PHE cc_start: 0.9212 (t80) cc_final: 0.8996 (t80)
REVERT: A 1016 ASP cc_start: 0.8747 (m-30) cc_final: 0.8430 (m-30)
REVERT: A 1057 MET cc_start: 0.8240 (tpp) cc_final: 0.7950 (tpp)
REVERT: A 1090 LEU cc_start: 0.9446 (tp) cc_final: 0.9046 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 148
  average time/residue: 0.0777
  time to fit residues: 17.5305
Evaluate side-chains
  114 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 112 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   chunk 98 optimal weight:   20.0000
   chunk 64 optimal weight:    3.9990
   chunk 96 optimal weight:    9.9990
   chunk 28 optimal weight:    0.5980
   chunk 31 optimal weight:    5.9990
   chunk 92 optimal weight:    0.0030
   chunk 106 optimal weight:    8.9990
   chunk 42 optimal weight:    3.9990
   chunk 93 optimal weight:    5.9990
   overall best weight:    1.2794

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.162721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.117289 restraints weight = 21022.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.115498 restraints weight = 11465.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.116689 restraints weight = 8451.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.117043 restraints weight = 7149.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.117211 restraints weight = 7095.075|
|-----------------------------------------------------------------------------|
r_work (final): 0.3548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.1440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9133  Z= 0.135
  Angle     :  0.573  10.140  12358  Z= 0.301
  Chirality :  0.042   0.162   1423
  Planarity :  0.003   0.036   1574
  Dihedral  :  4.239  21.400   1266
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.28 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  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 aren not related in a simple way.
  whole:  0.34 (0.26), residues: 1162
  helix:  1.49 (0.21), residues: 668
  sheet: -0.78 (0.89), residues: 39
  loop : -1.66 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1022 
 TYR   0.012   0.001   TYR A 717 
 PHE   0.033   0.001   PHE A 181 
 TRP   0.003   0.001   TRP A 108 
 HIS   0.002   0.001   HIS A 749 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 9133)
  covalent geometry    : angle       0.57325 (12358)
  hydrogen bonds       : bond        0.05544 (  475)
  hydrogen bonds       : angle       4.45748 ( 1386)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 ASP cc_start: 0.7643 (t0) cc_final: 0.7144 (t0)
REVERT: A  131 ASP cc_start: 0.8570 (t70) cc_final: 0.7949 (t0)
REVERT: A  266 MET cc_start: 0.8332 (tmm) cc_final: 0.7807 (tmm)
REVERT: A  416 PHE cc_start: 0.8081 (m-80) cc_final: 0.7793 (m-80)
REVERT: A  438 PHE cc_start: 0.9392 (t80) cc_final: 0.9189 (t80)
REVERT: A  711 MET cc_start: 0.7586 (ttt) cc_final: 0.7265 (ttm)
REVERT: A  855 LYS cc_start: 0.9137 (mmmt) cc_final: 0.8852 (mttp)
REVERT: A 1016 ASP cc_start: 0.8812 (m-30) cc_final: 0.8601 (m-30)
REVERT: A 1057 MET cc_start: 0.8372 (tpp) cc_final: 0.8073 (tpp)
REVERT: A 1090 LEU cc_start: 0.9521 (tp) cc_final: 0.9114 (tp)
REVERT: A 1155 GLN cc_start: 0.9437 (mp10) cc_final: 0.9164 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 0.0817
  time to fit residues: 18.0776
Evaluate side-chains
  111 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 76 optimal weight:    3.9990
   chunk 29 optimal weight:    0.5980
   chunk 113 optimal weight:    4.9990
   chunk 84 optimal weight:    2.9990
   chunk 57 optimal weight:    7.9990
   chunk 58 optimal weight:   10.0000
   chunk 54 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 36 optimal weight:   20.0000
   chunk 43 optimal weight:    6.9990
   chunk 94 optimal weight:    9.9990
   overall best weight:    2.3188

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

Flipped N/Q/H residues before XYZ refinement:
** A 115 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 = 0.4161 r_free = 0.4161 target = 0.161038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.116346 restraints weight = 20862.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.115648 restraints weight = 10206.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.116820 restraints weight = 7366.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.117102 restraints weight = 6410.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.117194 restraints weight = 6012.341|
|-----------------------------------------------------------------------------|
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.1658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9133  Z= 0.193
  Angle     :  0.627  10.021  12358  Z= 0.334
  Chirality :  0.043   0.164   1423
  Planarity :  0.004   0.040   1574
  Dihedral  :  4.394  22.467   1266
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.54 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  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 aren not related in a simple way.
  whole:  0.26 (0.26), residues: 1162
  helix:  1.38 (0.21), residues: 664
  sheet: -0.74 (0.92), residues: 33
  loop : -1.59 (0.28), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 440 
 TYR   0.016   0.002   TYR A 262 
 PHE   0.017   0.002   PHE A1061 
 TRP   0.004   0.001   TRP A 684 
 HIS   0.004   0.001   HIS A 749 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 ( 9133)
  covalent geometry    : angle       0.62663 (12358)
  hydrogen bonds       : bond        0.06140 (  475)
  hydrogen bonds       : angle       4.72735 ( 1386)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 ASP cc_start: 0.7660 (t0) cc_final: 0.7210 (t0)
REVERT: A  131 ASP cc_start: 0.8574 (t70) cc_final: 0.8042 (t70)
REVERT: A  266 MET cc_start: 0.8277 (tmm) cc_final: 0.7793 (tmm)
REVERT: A  711 MET cc_start: 0.7809 (ttt) cc_final: 0.7345 (ttm)
REVERT: A  855 LYS cc_start: 0.9161 (mmmt) cc_final: 0.8870 (mttp)
REVERT: A 1016 ASP cc_start: 0.8839 (m-30) cc_final: 0.8633 (m-30)
REVERT: A 1057 MET cc_start: 0.8347 (tpp) cc_final: 0.8073 (tpp)
REVERT: A 1070 MET cc_start: 0.8635 (tmm) cc_final: 0.8397 (tmm)
REVERT: A 1155 GLN cc_start: 0.9450 (mp10) cc_final: 0.9190 (mp10)
REVERT: A 1172 LEU cc_start: 0.8929 (mt) cc_final: 0.8710 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 146
  average time/residue: 0.0841
  time to fit residues: 18.0080
Evaluate side-chains
  112 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 75 optimal weight:    0.8980
   chunk 50 optimal weight:    8.9990
   chunk 109 optimal weight:   20.0000
   chunk 21 optimal weight:    0.7980
   chunk 17 optimal weight:    0.6980
   chunk 94 optimal weight:   20.0000
   chunk 4 optimal weight:    0.7980
   chunk 54 optimal weight:    0.4980
   chunk 18 optimal weight:    1.9990
   chunk 108 optimal weight:    9.9990
   chunk 7 optimal weight:    2.9990
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.166520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.121701 restraints weight = 20857.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.120836 restraints weight = 10705.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.121239 restraints weight = 7910.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.121811 restraints weight = 7079.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.122085 restraints weight = 6543.110|
|-----------------------------------------------------------------------------|
r_work (final): 0.3615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.1663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   9133  Z= 0.120
  Angle     :  0.568   9.854  12358  Z= 0.298
  Chirality :  0.041   0.150   1423
  Planarity :  0.003   0.035   1574
  Dihedral  :  4.319  21.493   1266
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.45 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  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 aren not related in a simple way.
  whole:  0.42 (0.26), residues: 1162
  helix:  1.52 (0.21), residues: 664
  sheet: -0.78 (0.88), residues: 39
  loop : -1.55 (0.29), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1022 
 TYR   0.017   0.001   TYR A 276 
 PHE   0.018   0.001   PHE A 305 
 TRP   0.004   0.000   TRP A 108 
 HIS   0.002   0.000   HIS A 749 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 9133)
  covalent geometry    : angle       0.56841 (12358)
  hydrogen bonds       : bond        0.05504 (  475)
  hydrogen bonds       : angle       4.37102 ( 1386)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 ASP cc_start: 0.7568 (t0) cc_final: 0.7171 (t0)
REVERT: A  131 ASP cc_start: 0.8510 (t70) cc_final: 0.8070 (t0)
REVERT: A  266 MET cc_start: 0.8211 (tmm) cc_final: 0.7703 (tmm)
REVERT: A  416 PHE cc_start: 0.8247 (m-80) cc_final: 0.7996 (m-80)
REVERT: A  711 MET cc_start: 0.7613 (ttt) cc_final: 0.7234 (ttm)
REVERT: A  855 LYS cc_start: 0.9028 (mmmt) cc_final: 0.8777 (mttp)
REVERT: A 1016 ASP cc_start: 0.8758 (m-30) cc_final: 0.8554 (m-30)
REVERT: A 1041 GLN cc_start: 0.9101 (tm-30) cc_final: 0.8309 (tm-30)
REVERT: A 1070 MET cc_start: 0.8690 (tmm) cc_final: 0.8471 (tmm)
REVERT: A 1155 GLN cc_start: 0.9423 (mp10) cc_final: 0.9175 (mp10)
REVERT: A 1172 LEU cc_start: 0.8859 (mt) cc_final: 0.8646 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 146
  average time/residue: 0.0858
  time to fit residues: 18.4868
Evaluate side-chains
  110 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 102 optimal weight:   10.0000
   chunk 79 optimal weight:    6.9990
   chunk 108 optimal weight:    5.9990
   chunk 14 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 1 optimal weight:    0.0270
   chunk 24 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   chunk 73 optimal weight:    2.9990
   chunk 58 optimal weight:    4.9990
   chunk 75 optimal weight:    0.4980
   overall best weight:    2.1044

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

Flipped N/Q/H residues before XYZ refinement:
** A 115 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 = 0.4176 r_free = 0.4176 target = 0.162270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.119945 restraints weight = 20984.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.122613 restraints weight = 12759.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.121714 restraints weight = 10378.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.121960 restraints weight = 7790.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.122366 restraints weight = 6800.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.1857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9133  Z= 0.184
  Angle     :  0.631   9.364  12358  Z= 0.334
  Chirality :  0.043   0.149   1423
  Planarity :  0.004   0.037   1574
  Dihedral  :  4.438  22.209   1266
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.80 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  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 aren not related in a simple way.
  whole:  0.29 (0.26), residues: 1162
  helix:  1.39 (0.21), residues: 666
  sheet: -0.90 (0.85), residues: 39
  loop : -1.56 (0.29), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 295 
 TYR   0.016   0.001   TYR A 238 
 PHE   0.023   0.002   PHE A 293 
 TRP   0.004   0.001   TRP A 108 
 HIS   0.003   0.001   HIS A 749 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 9133)
  covalent geometry    : angle       0.63112 (12358)
  hydrogen bonds       : bond        0.06020 (  475)
  hydrogen bonds       : angle       4.61337 ( 1386)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 ASP cc_start: 0.7553 (t0) cc_final: 0.7189 (t0)
REVERT: A   79 MET cc_start: 0.8350 (mmp) cc_final: 0.8017 (mmm)
REVERT: A  131 ASP cc_start: 0.8437 (t70) cc_final: 0.8039 (t70)
REVERT: A  240 TYR cc_start: 0.7744 (m-80) cc_final: 0.7465 (m-80)
REVERT: A  266 MET cc_start: 0.8211 (tmm) cc_final: 0.7675 (tmm)
REVERT: A  711 MET cc_start: 0.7694 (ttt) cc_final: 0.7301 (ttm)
REVERT: A 1016 ASP cc_start: 0.8749 (m-30) cc_final: 0.8452 (m-30)
REVERT: A 1041 GLN cc_start: 0.8889 (tm-30) cc_final: 0.8076 (tm-30)
REVERT: A 1057 MET cc_start: 0.8076 (tpp) cc_final: 0.7827 (tpp)
REVERT: A 1155 GLN cc_start: 0.9308 (mp10) cc_final: 0.9051 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.0868
  time to fit residues: 17.6720
Evaluate side-chains
  112 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 27 optimal weight:    0.8980
   chunk 72 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   chunk 65 optimal weight:    4.9990
   chunk 103 optimal weight:    5.9990
   chunk 69 optimal weight:    0.3980
   chunk 58 optimal weight:    2.9990
   chunk 91 optimal weight:    0.5980
   chunk 63 optimal weight:    0.9990
   chunk 37 optimal weight:   20.0000
   chunk 52 optimal weight:    9.9990
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.166768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.121847 restraints weight = 20881.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.121070 restraints weight = 10934.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.121562 restraints weight = 7813.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.122065 restraints weight = 7209.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.122296 restraints weight = 6760.094|
|-----------------------------------------------------------------------------|
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.1869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9133  Z= 0.125
  Angle     :  0.602   9.656  12358  Z= 0.314
  Chirality :  0.042   0.151   1423
  Planarity :  0.004   0.038   1574
  Dihedral  :  4.371  22.551   1266
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.63 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.35 (0.26), residues: 1162
  helix:  1.47 (0.21), residues: 668
  sheet: -0.80 (0.87), residues: 39
  loop : -1.61 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1007 
 TYR   0.011   0.001   TYR A 717 
 PHE   0.027   0.002   PHE A 181 
 TRP   0.005   0.001   TRP A 283 
 HIS   0.002   0.001   HIS A 749 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 9133)
  covalent geometry    : angle       0.60210 (12358)
  hydrogen bonds       : bond        0.05503 (  475)
  hydrogen bonds       : angle       4.36485 ( 1386)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 LEU cc_start: 0.6672 (mt) cc_final: 0.6405 (mt)
REVERT: A   75 ASP cc_start: 0.7565 (t0) cc_final: 0.7175 (t0)
REVERT: A  131 ASP cc_start: 0.8559 (t70) cc_final: 0.8033 (t0)
REVERT: A  266 MET cc_start: 0.8258 (tmm) cc_final: 0.7715 (tmm)
REVERT: A  416 PHE cc_start: 0.8118 (m-80) cc_final: 0.7856 (m-80)
REVERT: A  855 LYS cc_start: 0.9112 (mmmt) cc_final: 0.8838 (mppt)
REVERT: A 1070 MET cc_start: 0.8673 (tmm) cc_final: 0.8385 (tmm)
REVERT: A 1155 GLN cc_start: 0.9377 (mp10) cc_final: 0.9144 (mp10)
REVERT: A 1172 LEU cc_start: 0.8862 (mt) cc_final: 0.8613 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 146
  average time/residue: 0.0845
  time to fit residues: 18.2309
Evaluate side-chains
  117 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 48 optimal weight:    0.0040
   chunk 69 optimal weight:    6.9990
   chunk 80 optimal weight:    8.9990
   chunk 109 optimal weight:   20.0000
   chunk 88 optimal weight:    0.0270
   chunk 49 optimal weight:    0.9980
   chunk 14 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   chunk 113 optimal weight:    6.9990
   chunk 65 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   overall best weight:    0.9652

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

Flipped N/Q/H residues before XYZ refinement:
A  73 GLN
A 680 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.166573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.122477 restraints weight = 20883.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.122513 restraints weight = 12234.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.123111 restraints weight = 7877.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.123544 restraints weight = 6575.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.123640 restraints weight = 6035.882|
|-----------------------------------------------------------------------------|
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.1948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9133  Z= 0.128
  Angle     :  0.601   9.351  12358  Z= 0.317
  Chirality :  0.042   0.145   1423
  Planarity :  0.004   0.035   1574
  Dihedral  :  4.348  22.257   1266
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.54 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.63 %
    Favored  : 99.37 %
  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 aren not related in a simple way.
  whole:  0.36 (0.26), residues: 1162
  helix:  1.48 (0.21), residues: 668
  sheet: -0.91 (0.86), residues: 39
  loop : -1.60 (0.29), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 511 
 TYR   0.020   0.001   TYR A 276 
 PHE   0.018   0.001   PHE A 386 
 TRP   0.005   0.001   TRP A 108 
 HIS   0.002   0.000   HIS A 749 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 9133)
  covalent geometry    : angle       0.60097 (12358)
  hydrogen bonds       : bond        0.05404 (  475)
  hydrogen bonds       : angle       4.34174 ( 1386)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 LEU cc_start: 0.6623 (mt) cc_final: 0.6322 (mt)
REVERT: A   75 ASP cc_start: 0.7443 (t0) cc_final: 0.7164 (t0)
REVERT: A  131 ASP cc_start: 0.8494 (t70) cc_final: 0.8016 (t0)
REVERT: A  240 TYR cc_start: 0.7611 (m-80) cc_final: 0.7398 (m-80)
REVERT: A  266 MET cc_start: 0.8250 (tmm) cc_final: 0.7657 (tmm)
REVERT: A  416 PHE cc_start: 0.8116 (m-80) cc_final: 0.7862 (m-80)
REVERT: A  723 MET cc_start: 0.8623 (pmm) cc_final: 0.8180 (ptt)
REVERT: A  855 LYS cc_start: 0.9137 (mmmt) cc_final: 0.8887 (mppt)
REVERT: A 1016 ASP cc_start: 0.8724 (m-30) cc_final: 0.8458 (m-30)
REVERT: A 1070 MET cc_start: 0.8575 (tmm) cc_final: 0.8318 (tmm)
REVERT: A 1155 GLN cc_start: 0.9331 (mp10) cc_final: 0.9097 (mp10)
REVERT: A 1172 LEU cc_start: 0.8795 (mt) cc_final: 0.8571 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 146
  average time/residue: 0.0836
  time to fit residues: 18.0432
Evaluate side-chains
  119 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   chunk 111 optimal weight:   20.0000
   chunk 50 optimal weight:    2.9990
   chunk 54 optimal weight:    3.9990
   chunk 64 optimal weight:    0.3980
   chunk 2 optimal weight:    4.9990
   chunk 73 optimal weight:    0.9980
   chunk 71 optimal weight:    6.9990
   chunk 21 optimal weight:    0.9980
   chunk 112 optimal weight:    5.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** A 680 ASN ** 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 = 0.4220 r_free = 0.4220 target = 0.166093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.122577 restraints weight = 20969.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.121229 restraints weight = 10595.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.122736 restraints weight = 7862.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.123021 restraints weight = 6465.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.123142 restraints weight = 6245.316|
|-----------------------------------------------------------------------------|
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.2033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9133  Z= 0.128
  Angle     :  0.603   9.223  12358  Z= 0.317
  Chirality :  0.042   0.145   1423
  Planarity :  0.004   0.035   1574
  Dihedral  :  4.309  22.233   1266
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.37 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.42 %
    Favored  : 99.58 %
  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 aren not related in a simple way.
  whole:  0.35 (0.26), residues: 1162
  helix:  1.50 (0.21), residues: 668
  sheet: -0.97 (0.86), residues: 39
  loop : -1.64 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A1022 
 TYR   0.011   0.001   TYR A  86 
 PHE   0.019   0.001   PHE A 386 
 TRP   0.005   0.001   TRP A 108 
 HIS   0.002   0.000   HIS A 749 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 9133)
  covalent geometry    : angle       0.60260 (12358)
  hydrogen bonds       : bond        0.05310 (  475)
  hydrogen bonds       : angle       4.30821 ( 1386)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 LEU cc_start: 0.6569 (mt) cc_final: 0.6276 (mt)
REVERT: A   75 ASP cc_start: 0.7520 (t0) cc_final: 0.7132 (t0)
REVERT: A  266 MET cc_start: 0.8248 (tmm) cc_final: 0.7708 (tmm)
REVERT: A  386 PHE cc_start: 0.7645 (t80) cc_final: 0.7339 (t80)
REVERT: A  416 PHE cc_start: 0.8237 (m-80) cc_final: 0.8000 (m-80)
REVERT: A  723 MET cc_start: 0.8656 (pmm) cc_final: 0.8225 (ptt)
REVERT: A  855 LYS cc_start: 0.9108 (mmmt) cc_final: 0.8861 (mppt)
REVERT: A 1016 ASP cc_start: 0.8744 (m-30) cc_final: 0.8494 (m-30)
REVERT: A 1070 MET cc_start: 0.8614 (tmm) cc_final: 0.8337 (tmm)
REVERT: A 1155 GLN cc_start: 0.9340 (mp10) cc_final: 0.9110 (mp10)
REVERT: A 1172 LEU cc_start: 0.8746 (mt) cc_final: 0.8413 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 142
  average time/residue: 0.0794
  time to fit residues: 16.9910
Evaluate side-chains
  120 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 110 optimal weight:    3.9990
   chunk 114 optimal weight:   20.0000
   chunk 25 optimal weight:    3.9990
   chunk 4 optimal weight:    0.6980
   chunk 59 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   chunk 104 optimal weight:    0.9990
   chunk 77 optimal weight:    3.9990
   chunk 88 optimal weight:    0.0970
   chunk 30 optimal weight:    0.9990
   chunk 84 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 680 ASN ** 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 = 0.4242 r_free = 0.4242 target = 0.167871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.124032 restraints weight = 20785.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.123105 restraints weight = 11128.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.124482 restraints weight = 7756.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.124842 restraints weight = 6885.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.125790 restraints weight = 6396.043|
|-----------------------------------------------------------------------------|
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.2095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9133  Z= 0.119
  Angle     :  0.605   9.165  12358  Z= 0.314
  Chirality :  0.042   0.161   1423
  Planarity :  0.003   0.035   1574
  Dihedral  :  4.250  22.104   1266
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.88 %
    Favored  : 93.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  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 aren not related in a simple way.
  whole:  0.35 (0.26), residues: 1162
  helix:  1.50 (0.21), residues: 668
  sheet: -1.00 (0.86), residues: 39
  loop : -1.64 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A1022 
 TYR   0.008   0.001   TYR A 717 
 PHE   0.018   0.001   PHE A 200 
 TRP   0.006   0.001   TRP A 108 
 HIS   0.002   0.000   HIS A  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 9133)
  covalent geometry    : angle       0.60527 (12358)
  hydrogen bonds       : bond        0.05043 (  475)
  hydrogen bonds       : angle       4.18284 ( 1386)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1495.56 seconds
wall clock time: 26 minutes 40.73 seconds (1600.73 seconds total)