Starting phenix.real_space_refine
on Sat Jun  7 22:28:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kg2_62306/06_2025/9kg2_62306.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kg2_62306/06_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kg2_62306/06_2025/9kg2_62306.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kg2_62306/06_2025/9kg2_62306.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kg2_62306/06_2025/9kg2_62306.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kg2_62306/06_2025/9kg2_62306.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 5.48, per 1000 atoms: 0.61
  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: 2.28
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.99
  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: 2.90

  Time building geometry restraints manager: 2.71 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:                  0.000
  Normalize map: mean=0, sd=1:             0.890
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     23.600
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.730
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.26), 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
 TRP   0.005   0.001   TRP A 283 
 HIS   0.002   0.001   HIS A 749 
 PHE   0.020   0.001   PHE A 309 
 TYR   0.017   0.001   TYR A 205 
 ARG   0.009   0.001   ARG A1022 

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

*********************** 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  : 0.919 
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: 0.1688
  time to fit residues: 35.1055
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  : 0.901 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:    3.9990
   chunk 87 optimal weight:    0.6980
   chunk 48 optimal weight:    9.9990
   chunk 30 optimal weight:    6.9990
   chunk 59 optimal weight:    0.9980
   chunk 46 optimal weight:    6.9990
   chunk 90 optimal weight:    0.5980
   chunk 35 optimal weight:    5.9990
   chunk 55 optimal weight:   30.0000
   chunk 67 optimal weight:    2.9990
   chunk 105 optimal weight:    0.0670
   overall best weight:    1.0720

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.163041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.117343 restraints weight = 19538.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.115534 restraints weight = 12343.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.116534 restraints weight = 8686.078|
|-----------------------------------------------------------------------------|
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.0853

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= 0.130
  Angle     :  0.563  10.267  12358  Z= 0.299
  Chirality :  0.041   0.141   1423
  Planarity :  0.004   0.034   1574
  Dihedral  :  4.208  21.085   1266
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.85 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  6.53 %
    Favored  : 93.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.26), residues: 1162
  helix:  1.56 (0.21), residues: 661
  sheet: -0.72 (0.91), residues: 39
  loop : -1.53 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 108 
 HIS   0.004   0.001   HIS A1128 
 PHE   0.014   0.001   PHE A  36 
 TYR   0.012   0.001   TYR A  86 
 ARG   0.004   0.000   ARG A1223 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05488 (  475)
  hydrogen bonds       : angle       4.61768 ( 1386)
  covalent geometry    : bond        0.00263 ( 9133)
  covalent geometry    : angle       0.56303 (12358)

*********************** 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
  142 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 141
  time to evaluate  : 0.892 
Fit side-chains
REVERT: A   75 ASP cc_start: 0.7636 (t0) cc_final: 0.7182 (t0)
REVERT: A  205 TYR cc_start: 0.8725 (t80) cc_final: 0.8453 (t80)
REVERT: A  266 MET cc_start: 0.8364 (tmm) cc_final: 0.7912 (tmm)
REVERT: A  711 MET cc_start: 0.7637 (ttt) cc_final: 0.7414 (ttm)
REVERT: A 1090 LEU cc_start: 0.9485 (tp) cc_final: 0.9097 (tp)
REVERT: A 1110 LYS cc_start: 0.8771 (tmtt) cc_final: 0.8549 (tptp)
  outliers start: 1
  outliers final: 0
  residues processed: 142
  average time/residue: 0.1566
  time to fit residues: 33.5113
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  : 0.940 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 10 optimal weight:    5.9990
   chunk 98 optimal weight:   20.0000
   chunk 104 optimal weight:    5.9990
   chunk 82 optimal weight:    6.9990
   chunk 100 optimal weight:    0.2980
   chunk 89 optimal weight:    5.9990
   chunk 22 optimal weight:    6.9990
   chunk 74 optimal weight:    1.9990
   chunk 63 optimal weight:    0.5980
   chunk 84 optimal weight:    0.8980
   chunk 52 optimal weight:   10.0000
   overall best weight:    1.9584

-------------------------------------------------------------------------------
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**
A1128 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.159667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.115543 restraints weight = 21072.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.114710 restraints weight = 12261.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.115269 restraints weight = 10477.983|
|-----------------------------------------------------------------------------|
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.1337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9133  Z= 0.169
  Angle     :  0.597  10.273  12358  Z= 0.317
  Chirality :  0.042   0.152   1423
  Planarity :  0.004   0.038   1574
  Dihedral  :  4.296  21.917   1266
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.37 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.25), residues: 1162
  helix:  1.39 (0.21), residues: 664
  sheet: -0.55 (0.96), residues: 32
  loop : -1.61 (0.28), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 684 
 HIS   0.005   0.001   HIS A1128 
 PHE   0.019   0.002   PHE A 984 
 TYR   0.023   0.002   TYR A 276 
 ARG   0.006   0.000   ARG A1022 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05987 (  475)
  hydrogen bonds       : angle       4.65892 ( 1386)
  covalent geometry    : bond        0.00367 ( 9133)
  covalent geometry    : angle       0.59710 (12358)

*********************** 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: 0
    poor density    : 149
  time to evaluate  : 0.982 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 ASP cc_start: 0.7690 (t0) cc_final: 0.7241 (t0)
REVERT: A  266 MET cc_start: 0.8401 (tmm) cc_final: 0.7894 (tmm)
REVERT: A  711 MET cc_start: 0.7830 (ttt) cc_final: 0.7537 (ttm)
REVERT: A 1016 ASP cc_start: 0.8792 (m-30) cc_final: 0.8493 (m-30)
REVERT: A 1090 LEU cc_start: 0.9488 (tp) cc_final: 0.9119 (tp)
REVERT: A 1155 GLN cc_start: 0.9360 (mp10) cc_final: 0.9153 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 149
  average time/residue: 0.1783
  time to fit residues: 39.6445
Evaluate side-chains
  115 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.988 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 81 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 83 optimal weight:    1.9990
   chunk 67 optimal weight:    0.8980
   chunk 31 optimal weight:    5.9990
   chunk 90 optimal weight:    3.9990
   chunk 55 optimal weight:   20.0000
   chunk 18 optimal weight:    6.9990
   chunk 68 optimal weight:    1.9990
   chunk 25 optimal weight:    5.9990
   chunk 74 optimal weight:    0.9980
   overall best weight:    1.3384

-------------------------------------------------------------------------------
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 = 0.4169 r_free = 0.4169 target = 0.162203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.116454 restraints weight = 20662.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.115595 restraints weight = 10506.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.116735 restraints weight = 7930.459|
|-----------------------------------------------------------------------------|
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.1507

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= 0.135
  Angle     :  0.577  10.127  12358  Z= 0.303
  Chirality :  0.042   0.158   1423
  Planarity :  0.004   0.036   1574
  Dihedral  :  4.256  21.561   1266
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.45 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.26), residues: 1162
  helix:  1.45 (0.21), residues: 668
  sheet: -0.84 (0.89), residues: 39
  loop : -1.65 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 108 
 HIS   0.003   0.001   HIS A 749 
 PHE   0.030   0.001   PHE A 181 
 TYR   0.012   0.001   TYR A 717 
 ARG   0.003   0.000   ARG A1007 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05629 (  475)
  hydrogen bonds       : angle       4.48176 ( 1386)
  covalent geometry    : bond        0.00284 ( 9133)
  covalent geometry    : angle       0.57703 (12358)

*********************** 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
  150 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 1.041 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 LEU cc_start: 0.6549 (mt) cc_final: 0.6314 (mt)
REVERT: A   75 ASP cc_start: 0.7608 (t0) cc_final: 0.7111 (t0)
REVERT: A  131 ASP cc_start: 0.8536 (t70) cc_final: 0.8096 (t0)
REVERT: A  266 MET cc_start: 0.8336 (tmm) cc_final: 0.7824 (tmm)
REVERT: A  711 MET cc_start: 0.7741 (ttt) cc_final: 0.7541 (ttm)
REVERT: A  855 LYS cc_start: 0.9132 (mmmt) cc_final: 0.8746 (mtmm)
REVERT: A 1016 ASP cc_start: 0.8697 (m-30) cc_final: 0.8440 (m-30)
REVERT: A 1155 GLN cc_start: 0.9413 (mp10) cc_final: 0.9146 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 150
  average time/residue: 0.2038
  time to fit residues: 45.5603
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  : 1.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 11 optimal weight:    0.0970
   chunk 93 optimal weight:    9.9990
   chunk 72 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9990
   chunk 19 optimal weight:    7.9990
   chunk 61 optimal weight:    4.9990
   chunk 35 optimal weight:    5.9990
   chunk 5 optimal weight:    8.9990
   chunk 52 optimal weight:    4.9990
   chunk 45 optimal weight:    5.9990
   overall best weight:    1.8184

-------------------------------------------------------------------------------
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 = 0.4194 r_free = 0.4194 target = 0.163998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.120743 restraints weight = 20752.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.121611 restraints weight = 11811.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.121764 restraints weight = 8639.277|
|-----------------------------------------------------------------------------|
r_work (final): 0.3620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.1643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   9133  Z= 0.162
  Angle     :  0.602   9.882  12358  Z= 0.320
  Chirality :  0.042   0.162   1423
  Planarity :  0.004   0.037   1574
  Dihedral  :  4.371  21.847   1266
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.45 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.26), residues: 1162
  helix:  1.39 (0.21), residues: 666
  sheet: -0.87 (0.87), residues: 39
  loop : -1.63 (0.29), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 684 
 HIS   0.003   0.001   HIS A 749 
 PHE   0.020   0.002   PHE A 293 
 TYR   0.016   0.001   TYR A 238 
 ARG   0.005   0.000   ARG A 440 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05884 (  475)
  hydrogen bonds       : angle       4.58423 ( 1386)
  covalent geometry    : bond        0.00353 ( 9133)
  covalent geometry    : angle       0.60172 (12358)

*********************** 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
  145 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.993 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 ASP cc_start: 0.7578 (t0) cc_final: 0.7180 (t0)
REVERT: A  131 ASP cc_start: 0.8389 (t70) cc_final: 0.8039 (t70)
REVERT: A  266 MET cc_start: 0.8186 (tmm) cc_final: 0.7722 (tmm)
REVERT: A  711 MET cc_start: 0.7844 (ttt) cc_final: 0.7590 (ttm)
REVERT: A  855 LYS cc_start: 0.9150 (mmmt) cc_final: 0.8872 (mttp)
REVERT: A 1016 ASP cc_start: 0.8714 (m-30) cc_final: 0.8407 (m-30)
REVERT: A 1155 GLN cc_start: 0.9366 (mp10) cc_final: 0.9116 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 145
  average time/residue: 0.2764
  time to fit residues: 60.0958
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  : 1.713 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 100 optimal weight:    0.0070
   chunk 63 optimal weight:    0.0030
   chunk 40 optimal weight:    8.9990
   chunk 88 optimal weight:    0.0010
   chunk 0 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   chunk 84 optimal weight:    2.9990
   chunk 114 optimal weight:    0.4980
   chunk 112 optimal weight:    6.9990
   chunk 41 optimal weight:   10.0000
   chunk 87 optimal weight:    2.9990
   overall best weight:    0.7016

-------------------------------------------------------------------------------
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 = 0.4230 r_free = 0.4230 target = 0.166938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.122456 restraints weight = 20730.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.121401 restraints weight = 10763.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.122732 restraints weight = 7792.244|
|-----------------------------------------------------------------------------|
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.1735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9133  Z= 0.117
  Angle     :  0.563   9.731  12358  Z= 0.295
  Chirality :  0.041   0.147   1423
  Planarity :  0.003   0.034   1574
  Dihedral  :  4.287  21.756   1266
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.20 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.26), residues: 1162
  helix:  1.56 (0.21), residues: 666
  sheet: -0.75 (0.89), residues: 39
  loop : -1.62 (0.29), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 283 
 HIS   0.002   0.000   HIS A 749 
 PHE   0.031   0.001   PHE A 287 
 TYR   0.015   0.001   TYR A 276 
 ARG   0.007   0.000   ARG A1022 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05302 (  475)
  hydrogen bonds       : angle       4.27683 ( 1386)
  covalent geometry    : bond        0.00233 ( 9133)
  covalent geometry    : angle       0.56301 (12358)

*********************** 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
  144 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 1.046 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 LEU cc_start: 0.6552 (mt) cc_final: 0.6292 (mt)
REVERT: A   75 ASP cc_start: 0.7431 (t0) cc_final: 0.7024 (t0)
REVERT: A  131 ASP cc_start: 0.8452 (t70) cc_final: 0.7988 (t0)
REVERT: A  266 MET cc_start: 0.8234 (tmm) cc_final: 0.7702 (tmm)
REVERT: A  386 PHE cc_start: 0.8320 (t80) cc_final: 0.8090 (t80)
REVERT: A  855 LYS cc_start: 0.9033 (mmmt) cc_final: 0.8773 (mttp)
REVERT: A 1016 ASP cc_start: 0.8728 (m-30) cc_final: 0.8505 (m-30)
REVERT: A 1041 GLN cc_start: 0.9076 (tm-30) cc_final: 0.8262 (tm-30)
REVERT: A 1070 MET cc_start: 0.8617 (tmm) cc_final: 0.8402 (tmm)
REVERT: A 1155 GLN cc_start: 0.9389 (mp10) cc_final: 0.9139 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 144
  average time/residue: 0.2724
  time to fit residues: 58.8122
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  : 1.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 25 optimal weight:    5.9990
   chunk 74 optimal weight:    0.5980
   chunk 86 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 60 optimal weight:   10.0000
   chunk 47 optimal weight:    9.9990
   chunk 30 optimal weight:    5.9990
   chunk 45 optimal weight:   20.0000
   chunk 15 optimal weight:    0.9990
   overall best weight:    1.0184

-------------------------------------------------------------------------------
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 = 0.4228 r_free = 0.4228 target = 0.166808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.124575 restraints weight = 20980.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.125180 restraints weight = 11533.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.125563 restraints weight = 8801.269|
|-----------------------------------------------------------------------------|
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.1806

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= 0.124
  Angle     :  0.577   9.566  12358  Z= 0.303
  Chirality :  0.042   0.147   1423
  Planarity :  0.003   0.036   1574
  Dihedral  :  4.261  22.224   1266
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.80 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.26), residues: 1162
  helix:  1.55 (0.21), residues: 666
  sheet: -0.78 (0.87), residues: 39
  loop : -1.59 (0.29), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 108 
 HIS   0.002   0.000   HIS A 749 
 PHE   0.020   0.001   PHE A 305 
 TYR   0.016   0.001   TYR A 238 
 ARG   0.007   0.000   ARG A1022 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05282 (  475)
  hydrogen bonds       : angle       4.28334 ( 1386)
  covalent geometry    : bond        0.00259 ( 9133)
  covalent geometry    : angle       0.57700 (12358)

*********************** 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
  145 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.901 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 LEU cc_start: 0.6666 (mt) cc_final: 0.6437 (mt)
REVERT: A   75 ASP cc_start: 0.7430 (t0) cc_final: 0.7113 (t0)
REVERT: A  131 ASP cc_start: 0.8448 (t70) cc_final: 0.8071 (t0)
REVERT: A  266 MET cc_start: 0.8269 (tmm) cc_final: 0.7699 (tmm)
REVERT: A  855 LYS cc_start: 0.9151 (mmmt) cc_final: 0.8798 (mttp)
REVERT: A 1016 ASP cc_start: 0.8659 (m-30) cc_final: 0.8379 (m-30)
REVERT: A 1041 GLN cc_start: 0.8959 (tm-30) cc_final: 0.8108 (tm-30)
REVERT: A 1070 MET cc_start: 0.8487 (tmm) cc_final: 0.8268 (tmm)
REVERT: A 1155 GLN cc_start: 0.9297 (mp10) cc_final: 0.9059 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 145
  average time/residue: 0.1659
  time to fit residues: 35.8867
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  : 0.935 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 55 optimal weight:    9.9990
   chunk 74 optimal weight:    0.4980
   chunk 22 optimal weight:    0.8980
   chunk 73 optimal weight:    0.8980
   chunk 70 optimal weight:    0.5980
   chunk 67 optimal weight:    0.7980
   chunk 27 optimal weight:    5.9990
   chunk 113 optimal weight:    1.9990
   chunk 36 optimal weight:   10.0000
   chunk 68 optimal weight:    0.7980
   chunk 8 optimal weight:    3.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.4227 r_free = 0.4227 target = 0.166976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.123868 restraints weight = 20834.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.124116 restraints weight = 9866.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.125000 restraints weight = 6934.425|
|-----------------------------------------------------------------------------|
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.1880

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= 0.116
  Angle     :  0.577   9.293  12358  Z= 0.301
  Chirality :  0.041   0.144   1423
  Planarity :  0.003   0.033   1574
  Dihedral  :  4.249  21.626   1266
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.20 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.26), residues: 1162
  helix:  1.55 (0.21), residues: 668
  sheet: -0.72 (0.88), residues: 39
  loop : -1.64 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 108 
 HIS   0.002   0.000   HIS A 749 
 PHE   0.017   0.001   PHE A 305 
 TYR   0.010   0.001   TYR A 262 
 ARG   0.008   0.000   ARG A1022 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05069 (  475)
  hydrogen bonds       : angle       4.20674 ( 1386)
  covalent geometry    : bond        0.00233 ( 9133)
  covalent geometry    : angle       0.57668 (12358)

*********************** 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  : 0.892 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 ASP cc_start: 0.7363 (t0) cc_final: 0.7032 (t0)
REVERT: A  131 ASP cc_start: 0.8523 (t70) cc_final: 0.8044 (t0)
REVERT: A  266 MET cc_start: 0.8314 (tmm) cc_final: 0.7756 (tmm)
REVERT: A 1016 ASP cc_start: 0.8753 (m-30) cc_final: 0.8546 (m-30)
REVERT: A 1041 GLN cc_start: 0.8980 (tm-30) cc_final: 0.8276 (tm-30)
REVERT: A 1070 MET cc_start: 0.8645 (tmm) cc_final: 0.8383 (tmm)
REVERT: A 1155 GLN cc_start: 0.9333 (mp10) cc_final: 0.9103 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 146
  average time/residue: 0.1737
  time to fit residues: 37.3872
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  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 26 optimal weight:    4.9990
   chunk 113 optimal weight:   20.0000
   chunk 66 optimal weight:    0.8980
   chunk 47 optimal weight:    0.8980
   chunk 97 optimal weight:    5.9990
   chunk 1 optimal weight:    0.5980
   chunk 98 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   chunk 32 optimal weight:   10.0000
   chunk 81 optimal weight:    6.9990
   chunk 8 optimal weight:    2.9990
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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 = 0.4230 r_free = 0.4230 target = 0.167046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.123057 restraints weight = 20995.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.121745 restraints weight = 11122.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.122727 restraints weight = 7980.576|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.1913

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= 0.124
  Angle     :  0.588   9.516  12358  Z= 0.306
  Chirality :  0.041   0.151   1423
  Planarity :  0.003   0.034   1574
  Dihedral  :  4.231  23.375   1266
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.45 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.26), residues: 1162
  helix:  1.56 (0.21), residues: 669
  sheet: -0.76 (0.88), residues: 39
  loop : -1.61 (0.28), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 108 
 HIS   0.002   0.000   HIS A 749 
 PHE   0.022   0.001   PHE A 386 
 TYR   0.019   0.001   TYR A 102 
 ARG   0.008   0.000   ARG A1022 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05141 (  475)
  hydrogen bonds       : angle       4.20763 ( 1386)
  covalent geometry    : bond        0.00259 ( 9133)
  covalent geometry    : angle       0.58756 (12358)

*********************** 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
  140 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 1.012 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 ASP cc_start: 0.7441 (t0) cc_final: 0.7115 (t0)
REVERT: A  131 ASP cc_start: 0.8506 (t70) cc_final: 0.7889 (t0)
REVERT: A  266 MET cc_start: 0.8258 (tmm) cc_final: 0.7709 (tmm)
REVERT: A  386 PHE cc_start: 0.7851 (t80) cc_final: 0.7339 (t80)
REVERT: A 1016 ASP cc_start: 0.8790 (m-30) cc_final: 0.8578 (m-30)
REVERT: A 1041 GLN cc_start: 0.8978 (tm-30) cc_final: 0.8162 (tm-30)
REVERT: A 1070 MET cc_start: 0.8704 (tmm) cc_final: 0.8454 (tmm)
REVERT: A 1155 GLN cc_start: 0.9319 (mp10) cc_final: 0.9100 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.1831
  time to fit residues: 38.9079
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  : 0.924 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 15 optimal weight:    0.7980
   chunk 5 optimal weight:   10.0000
   chunk 54 optimal weight:    9.9990
   chunk 103 optimal weight:    0.8980
   chunk 100 optimal weight:    3.9990
   chunk 94 optimal weight:   20.0000
   chunk 57 optimal weight:   20.0000
   chunk 27 optimal weight:    5.9990
   chunk 92 optimal weight:    0.5980
   chunk 90 optimal weight:    4.9990
   chunk 72 optimal weight:    0.6980
   overall best weight:    1.3982

-------------------------------------------------------------------------------
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 = 0.4224 r_free = 0.4224 target = 0.166616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.124088 restraints weight = 21223.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.123969 restraints weight = 12361.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.124295 restraints weight = 10749.028|
|-----------------------------------------------------------------------------|
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
moved from start:          0.1969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9133  Z= 0.140
  Angle     :  0.602   9.173  12358  Z= 0.318
  Chirality :  0.042   0.145   1423
  Planarity :  0.003   0.034   1574
  Dihedral  :  4.287  22.664   1266
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.63 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.26), residues: 1162
  helix:  1.47 (0.21), residues: 669
  sheet: -0.77 (0.87), residues: 39
  loop : -1.59 (0.29), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 288 
 HIS   0.003   0.001   HIS A  51 
 PHE   0.024   0.002   PHE A 822 
 TYR   0.019   0.001   TYR A 238 
 ARG   0.008   0.000   ARG A1022 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05411 (  475)
  hydrogen bonds       : angle       4.31677 ( 1386)
  covalent geometry    : bond        0.00301 ( 9133)
  covalent geometry    : angle       0.60184 (12358)

********************** 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
  141 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 1.008 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 ASP cc_start: 0.7520 (t0) cc_final: 0.7176 (t0)
REVERT: A  266 MET cc_start: 0.8285 (tmm) cc_final: 0.7704 (tmm)
REVERT: A  386 PHE cc_start: 0.7760 (t80) cc_final: 0.7278 (t80)
REVERT: A  855 LYS cc_start: 0.9151 (mmmt) cc_final: 0.8877 (mppt)
REVERT: A 1016 ASP cc_start: 0.8814 (m-30) cc_final: 0.8556 (m-30)
REVERT: A 1041 GLN cc_start: 0.8886 (tm-30) cc_final: 0.8010 (tm-30)
REVERT: A 1155 GLN cc_start: 0.9272 (mp10) cc_final: 0.9065 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 141
  average time/residue: 0.1805
  time to fit residues: 37.6189
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  : 0.970 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 106 optimal weight:   10.0000
   chunk 23 optimal weight:    0.0370
   chunk 105 optimal weight:    2.9990
   chunk 74 optimal weight:    0.3980
   chunk 85 optimal weight:    1.9990
   chunk 109 optimal weight:   20.0000
   chunk 80 optimal weight:    5.9990
   chunk 38 optimal weight:   20.0000
   chunk 7 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 114 optimal weight:   20.0000
   overall best weight:    1.0662

-------------------------------------------------------------------------------
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 = 0.4222 r_free = 0.4222 target = 0.166414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.122568 restraints weight = 21152.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.121219 restraints weight = 10874.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.122202 restraints weight = 7951.155|
|-----------------------------------------------------------------------------|
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.2054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9133  Z= 0.128
  Angle     :  0.599   9.099  12358  Z= 0.313
  Chirality :  0.042   0.144   1423
  Planarity :  0.003   0.034   1574
  Dihedral  :  4.267  22.620   1266
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.88 %
    Favored  : 93.03 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.26), residues: 1162
  helix:  1.50 (0.21), residues: 669
  sheet: -0.78 (0.88), residues: 39
  loop : -1.61 (0.29), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 288 
 HIS   0.002   0.000   HIS A 749 
 PHE   0.019   0.002   PHE A 386 
 TYR   0.022   0.001   TYR A 276 
 ARG   0.007   0.000   ARG A1022 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05312 (  475)
  hydrogen bonds       : angle       4.20567 ( 1386)
  covalent geometry    : bond        0.00271 ( 9133)
  covalent geometry    : angle       0.59914 (12358)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2772.25 seconds
wall clock time: 50 minutes 18.85 seconds (3018.85 seconds total)