Starting phenix.real_space_refine
on Wed Mar  4 00:33:47 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zk4_14754/03_2026/7zk4_14754.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zk4_14754/03_2026/7zk4_14754.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zk4_14754/03_2026/7zk4_14754.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zk4_14754/03_2026/7zk4_14754.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zk4_14754/03_2026/7zk4_14754.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zk4_14754/03_2026/7zk4_14754.cif"
  }
  resolution = 2.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.056
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      31      5.16       5
     C    6028      2.51       5
     N    1554      2.21       5
     O    1716      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9337
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9094
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1176, 9094
          Classifications: {'peptide': 1176}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 29, 'TRANS': 1146}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 33
          Unresolved non-hydrogen angles: 40
          Unresolved non-hydrogen dihedrals: 26
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 16
    Chain: "A"
      Number of atoms: 243
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 243
          Unusual residues: {' MG': 2, 'ATP': 2, 'Y01': 5}
          Classifications: {'undetermined': 9, 'water': 4}
          Link IDs: {None: 12}
  Time building chain proxies: 2.09, per 1000 atoms: 0.22
  Number of scatterers: 9337
  At special positions: 0
  Unit cell: (71.982, 87.048, 148.986, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      31     16.00
     P       6     15.00
     Mg      2     11.99
     O    1716      8.00
     N    1554      7.00
     C    6028      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: 0.77
  Conformation dependent library (CDL) restraints added in 420.4 milliseconds
  

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2158

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 4 sheets defined
      71.9% alpha, 7.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 42 through 69
      removed outlier: 3.805A  pdb=" N   ASP A  46 " --> pdb=" O   ALA A  42 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   LEU A  64 " --> pdb=" O   HIS A  60 " (cutoff:3.500A)
      Proline residue:  A  65  - end of helix
    Processing helix  chain 'A' and resid 74 through 83
      removed outlier: 3.524A  pdb=" N   VAL A  81 " --> pdb=" O   SER A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 154
      removed outlier: 6.143A  pdb=" N   ARG A  97 " --> pdb=" O   GLU A  93 " (cutoff:3.500A)
      removed outlier: 5.015A  pdb=" N   ALA A  98 " --> pdb=" O   ALA A  94 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   GLN A 154 " --> pdb=" O   ALA A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 162
    Processing helix  chain 'A' and resid 163 through 165
      No H-bonds generated for 'chain 'A' and resid 163 through 165'
    Processing helix  chain 'A' and resid 166 through 180
      removed outlier: 4.216A  pdb=" N   VAL A 175 " --> pdb=" O   LEU A 171 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   SER A 176 " --> pdb=" O   THR A 172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 208
      removed outlier: 3.854A  pdb=" N   GLY A 187 " --> pdb=" O   GLY A 183 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   TRP A 208 " --> pdb=" O   PHE A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 216
      removed outlier: 3.508A  pdb=" N   VAL A 213 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 256
    Processing helix  chain 'A' and resid 256 through 263
    Processing helix  chain 'A' and resid 265 through 319
    Processing helix  chain 'A' and resid 323 through 344
    Processing helix  chain 'A' and resid 344 through 367
      removed outlier: 3.756A  pdb=" N   TYR A 359 " --> pdb=" O   ARG A 355 " (cutoff:3.500A)
      removed outlier: 5.163A  pdb=" N   GLU A 360 " --> pdb=" O   GLY A 356 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   VAL A 361 " --> pdb=" O   ALA A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 401
      removed outlier: 3.946A  pdb=" N   LYS A 401 " --> pdb=" O   PRO A 398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 428 through 437
      removed outlier: 3.511A  pdb=" N   GLN A 437 " --> pdb=" O   VAL A 433 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 458 through 465
    Processing helix  chain 'A' and resid 479 through 486
    Processing helix  chain 'A' and resid 492 through 503
    Processing helix  chain 'A' and resid 505 through 512
    Processing helix  chain 'A' and resid 514 through 518
      removed outlier: 3.752A  pdb=" N   THR A 518 " --> pdb=" O   GLN A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 521 through 525
    Processing helix  chain 'A' and resid 528 through 542
    Processing helix  chain 'A' and resid 558 through 572
      removed outlier: 3.700A  pdb=" N   ALA A 572 " --> pdb=" O   ALA A 568 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 584 through 590
      removed outlier: 3.567A  pdb=" N   VAL A 588 " --> pdb=" O   ARG A 584 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   ASN A 590 " --> pdb=" O   SER A 586 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 607 through 615
    Processing helix  chain 'A' and resid 616 through 624
      removed outlier: 3.503A  pdb=" N   LYS A 620 " --> pdb=" O   GLY A 616 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 691 through 699
    Processing helix  chain 'A' and resid 700 through 702
      No H-bonds generated for 'chain 'A' and resid 700 through 702'
    Processing helix  chain 'A' and resid 703 through 737
      removed outlier: 3.678A  pdb=" N   ASN A 717 " --> pdb=" O   ALA A 713 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   GLN A 721 " --> pdb=" O   ASN A 717 " (cutoff:3.500A)
      Proline residue:  A 722  - end of helix
      removed outlier: 4.073A  pdb=" N   SER A 725 " --> pdb=" O   GLN A 721 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   VAL A 726 " --> pdb=" O   PRO A 722 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 740 through 795
      removed outlier: 3.548A  pdb=" N   PHE A 773 " --> pdb=" O   GLN A 769 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 796 through 802
      removed outlier: 3.534A  pdb=" N   PHE A 800 " --> pdb=" O   ASP A 796 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 806 through 825
      removed outlier: 3.932A  pdb=" N   ALA A 824 " --> pdb=" O   GLN A 820 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   THR A 825 " --> pdb=" O   VAL A 821 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 826 through 850
      removed outlier: 3.820A  pdb=" N   GLY A 842 " --> pdb=" O   ASN A 838 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   ILE A 843 " --> pdb=" O   LEU A 839 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   ILE A 844 " --> pdb=" O   GLY A 840 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 853 through 899
      removed outlier: 4.077A  pdb=" N   LEU A 857 " --> pdb=" O   LEU A 853 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   LEU A 858 " --> pdb=" O   THR A 854 " (cutoff:3.500A)
      Proline residue:  A 862  - end of helix
      removed outlier: 3.871A  pdb=" N   GLU A 871 " --> pdb=" O   ALA A 867 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   LYS A 881 " --> pdb=" O   GLY A 877 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 899 through 906
    Processing helix  chain 'A' and resid 908 through 919
    Processing helix  chain 'A' and resid 920 through 962
      removed outlier: 3.706A  pdb=" N   HIS A 932 " --> pdb=" O   MET A 928 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 966 through 982
    Processing helix  chain 'A' and resid 983 through 990
    Processing helix  chain 'A' and resid 990 through 1009
      removed outlier: 3.522A  pdb=" N   LYS A 996 " --> pdb=" O   PRO A 992 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1071 through 1080
      removed outlier: 3.631A  pdb=" N   VAL A1076 " --> pdb=" O   LYS A1072 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1101 through 1108
    Processing helix  chain 'A' and resid 1122 through 1129
    Processing helix  chain 'A' and resid 1137 through 1148
    Processing helix  chain 'A' and resid 1150 through 1157
    Processing helix  chain 'A' and resid 1159 through 1163
    Processing helix  chain 'A' and resid 1166 through 1170
      removed outlier: 3.525A  pdb=" N   THR A1170 " --> pdb=" O   ASP A1167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1173 through 1188
      removed outlier: 3.976A  pdb=" N   ARG A1188 " --> pdb=" O   ARG A1184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1203 through 1217
    Processing helix  chain 'A' and resid 1229 through 1233
    Processing helix  chain 'A' and resid 1252 through 1259
      removed outlier: 3.512A  pdb=" N   GLN A1259 " --> pdb=" O   GLN A1255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1261 through 1269
    Processing sheet with id=AA1, first strand: chain 'A' and resid 406 through 413
      removed outlier: 6.789A  pdb=" N   LYS A 407 " --> pdb=" O   HIS A 394 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   HIS A 394 " --> pdb=" O   LYS A 407 " (cutoff:3.500A)
      removed outlier: 5.025A  pdb=" N   LEU A 409 " --> pdb=" O   ASN A 392 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   ILE A 393 " --> pdb=" O   ASP A 444 " (cutoff:3.500A)
      removed outlier: 6.378A  pdb=" N   ASP A 444 " --> pdb=" O   ILE A 393 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 466 through 469
      removed outlier: 6.489A  pdb=" N   GLY A 467 " --> pdb=" O   LEU A 549 " (cutoff:3.500A)
      removed outlier: 7.817A  pdb=" N   ASP A 551 " --> pdb=" O   GLY A 467 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   VAL A 469 " --> pdb=" O   ASP A 551 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   LEU A 548 " --> pdb=" O   ILE A 579 " (cutoff:3.500A)
      removed outlier: 7.754A  pdb=" N   ILE A 581 " --> pdb=" O   LEU A 548 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   LEU A 550 " --> pdb=" O   ILE A 581 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   GLU A 604 " --> pdb=" O   GLY A 596 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   ASP A 598 " --> pdb=" O   ILE A 602 " (cutoff:3.500A)
      removed outlier: 4.940A  pdb=" N   ILE A 602 " --> pdb=" O   ASP A 598 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1049 through 1056
      removed outlier: 6.881A  pdb=" N   GLN A1050 " --> pdb=" O   VAL A1037 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   VAL A1037 " --> pdb=" O   GLN A1050 " (cutoff:3.500A)
      removed outlier: 4.801A  pdb=" N   LEU A1052 " --> pdb=" O   GLY A1035 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   VAL A1036 " --> pdb=" O   ALA A1087 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   ALA A1087 " --> pdb=" O   VAL A1036 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1109 through 1112
      removed outlier: 6.384A  pdb=" N   GLY A1110 " --> pdb=" O   LEU A1194 " (cutoff:3.500A)
      removed outlier: 7.445A  pdb=" N   ASP A1196 " --> pdb=" O   GLY A1110 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   VAL A1112 " --> pdb=" O   ASP A1196 " (cutoff:3.500A)
      removed outlier: 6.139A  pdb=" N   LEU A1193 " --> pdb=" O   ILE A1224 " (cutoff:3.500A)
      removed outlier: 7.580A  pdb=" N   ILE A1226 " --> pdb=" O   LEU A1193 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   LEU A1195 " --> pdb=" O   ILE A1226 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   LEU A1062 " --> pdb=" O   VAL A1225 " (cutoff:3.500A)
      removed outlier: 6.062A  pdb=" N   THR A1061 " --> pdb=" O   LEU A1238 " (cutoff:3.500A)
      removed outlier: 7.485A  pdb=" N   VAL A1240 " --> pdb=" O   THR A1061 " (cutoff:3.500A)
      removed outlier: 6.258A  pdb=" N   ALA A1063 " --> pdb=" O   VAL A1240 " (cutoff:3.500A)
      removed outlier: 7.109A  pdb=" N   ILE A1242 " --> pdb=" O   ALA A1063 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   VAL A1065 " --> pdb=" O   ILE A1242 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   GLU A1249 " --> pdb=" O   VAL A1241 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   GLN A1243 " --> pdb=" O   VAL A1247 " (cutoff:3.500A)
      removed outlier: 5.008A  pdb=" N   VAL A1247 " --> pdb=" O   GLN A1243 " (cutoff:3.500A)

    631 hydrogen bonds defined for protein.
    1851 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: 1.52

  Time building geometry restraints manager: 0.99 seconds

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

  Histogram of bond lengths:
        1.15 -     1.28: 1509
        1.28 -     1.42: 2367
        1.42 -     1.55: 5560
        1.55 -     1.69: 21
        1.69 -     1.82: 61
  Bond restraints: 9518
  Sorted by residual:
  bond pdb=" C   LEU A  48 "
       pdb=" O   LEU A  48 "
    ideal  model  delta    sigma   weight residual
    1.236  1.146  0.090 1.29e-02 6.01e+03 4.89e+01
  bond pdb=" C   HIS A 932 "
       pdb=" O   HIS A 932 "
    ideal  model  delta    sigma   weight residual
    1.237  1.158  0.079 1.19e-02 7.06e+03 4.37e+01
  bond pdb=" C   MET A 928 "
       pdb=" O   MET A 928 "
    ideal  model  delta    sigma   weight residual
    1.236  1.157  0.080 1.26e-02 6.30e+03 3.99e+01
  bond pdb=" C   LEU A 134 "
       pdb=" O   LEU A 134 "
    ideal  model  delta    sigma   weight residual
    1.237  1.166  0.070 1.19e-02 7.06e+03 3.47e+01
  bond pdb=" CA  ALA A 943 "
       pdb=" CB  ALA A 943 "
    ideal  model  delta    sigma   weight residual
    1.531  1.446  0.085 1.59e-02 3.96e+03 2.84e+01
  ... (remaining 9513 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.06: 12706
        3.06 -     6.11: 184
        6.11 -     9.17: 18
        9.17 -    12.22: 3
       12.22 -    15.28: 2
  Bond angle restraints: 12913
  Sorted by residual:
  angle pdb=" N   ILE A 127 "
        pdb=" CA  ILE A 127 "
        pdb=" C   ILE A 127 "
      ideal   model   delta    sigma   weight residual
     111.00  101.28    9.72 1.09e+00 8.42e-01 7.95e+01
  angle pdb=" N   SER A  88 "
        pdb=" CA  SER A  88 "
        pdb=" C   SER A  88 "
      ideal   model   delta    sigma   weight residual
     111.07  103.21    7.86 1.07e+00 8.73e-01 5.40e+01
  angle pdb=" N   MET A  91 "
        pdb=" CA  MET A  91 "
        pdb=" C   MET A  91 "
      ideal   model   delta    sigma   weight residual
     111.54  101.60    9.94 1.36e+00 5.41e-01 5.34e+01
  angle pdb=" O2B ATP A2001 "
        pdb=" PB  ATP A2001 "
        pdb=" O3B ATP A2001 "
      ideal   model   delta    sigma   weight residual
     106.94  119.22  -12.28 1.88e+00 2.83e-01 4.27e+01
  angle pdb=" C   ARG A 954 "
        pdb=" CA  ARG A 954 "
        pdb=" CB  ARG A 954 "
      ideal   model   delta    sigma   weight residual
     110.85  100.62   10.23 1.70e+00 3.46e-01 3.62e+01
  ... (remaining 12908 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.49: 5554
       23.49 -    46.98: 305
       46.98 -    70.47: 54
       70.47 -    93.96: 19
       93.96 -   117.44: 3
  Dihedral angle restraints: 5935
    sinusoidal: 2567
      harmonic: 3368
  Sorted by residual:
  dihedral pdb=" C   ARG A 954 "
           pdb=" N   ARG A 954 "
           pdb=" CA  ARG A 954 "
           pdb=" CB  ARG A 954 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -107.79  -14.81     0      2.50e+00 1.60e-01 3.51e+01
  dihedral pdb=" C   ILE A 860 "
           pdb=" N   ILE A 860 "
           pdb=" CA  ILE A 860 "
           pdb=" CB  ILE A 860 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -134.06   12.06     0      2.50e+00 1.60e-01 2.33e+01
  dihedral pdb=" C   TYR A 946 "
           pdb=" N   TYR A 946 "
           pdb=" CA  TYR A 946 "
           pdb=" CB  TYR A 946 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.22   11.62     0      2.50e+00 1.60e-01 2.16e+01
  ... (remaining 5932 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.075: 1328
       0.075 -    0.151: 134
       0.151 -    0.226: 18
       0.226 -    0.302: 6
       0.302 -    0.377: 4
  Chirality restraints: 1490
  Sorted by residual:
  chirality pdb=" CA  TYR A 946 "
            pdb=" N   TYR A 946 "
            pdb=" C   TYR A 946 "
            pdb=" CB  TYR A 946 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.56e+00
  chirality pdb=" CA  ARG A 954 "
            pdb=" N   ARG A 954 "
            pdb=" C   ARG A 954 "
            pdb=" CB  ARG A 954 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.85   -0.34 2.00e-01 2.50e+01 2.81e+00
  chirality pdb=" CA  ILE A 860 "
            pdb=" N   ILE A 860 "
            pdb=" C   ILE A 860 "
            pdb=" CB  ILE A 860 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.11    0.33 2.00e-01 2.50e+01 2.69e+00
  ... (remaining 1487 not shown)

  Planarity restraints: 1606
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 858 "   -0.023 2.00e-02 2.50e+03   4.67e-02 2.18e+01
        pdb=" C   LEU A 858 "    0.081 2.00e-02 2.50e+03
        pdb=" O   LEU A 858 "   -0.030 2.00e-02 2.50e+03
        pdb=" N   ALA A 859 "   -0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 860 "   -0.021 2.00e-02 2.50e+03   4.26e-02 1.81e+01
        pdb=" C   ILE A 860 "    0.074 2.00e-02 2.50e+03
        pdb=" O   ILE A 860 "   -0.027 2.00e-02 2.50e+03
        pdb=" N   VAL A 861 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A  79 "   -0.018 2.00e-02 2.50e+03   3.71e-02 1.38e+01
        pdb=" C   ALA A  79 "    0.064 2.00e-02 2.50e+03
        pdb=" O   ALA A  79 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   SER A  80 "   -0.022 2.00e-02 2.50e+03
  ... (remaining 1603 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 73
        2.59 -     3.16: 8192
        3.16 -     3.74: 15320
        3.74 -     4.32: 21459
        4.32 -     4.90: 34768
  Nonbonded interactions: 79812
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 430 "
            pdb="MG    MG A2002 "
     model   vdw
     2.008 2.170
  nonbonded pdb="MG    MG A2004 "
            pdb=" O   HOH A2102 "
     model   vdw
     2.053 2.170
  nonbonded pdb="MG    MG A2002 "
            pdb=" O   HOH A2101 "
     model   vdw
     2.061 2.170
  nonbonded pdb="MG    MG A2002 "
            pdb=" O   HOH A2103 "
     model   vdw
     2.063 2.170
  nonbonded pdb=" OG  SER A1073 "
            pdb="MG    MG A2004 "
     model   vdw
     2.076 2.170
  ... (remaining 79807 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.640
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.900
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
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      :  0.006   0.092   9518  Z= 0.414
  Angle     :  0.861  15.278  12913  Z= 0.554
  Chirality :  0.053   0.377   1490
  Planarity :  0.005   0.047   1606
  Dihedral  : 15.323 117.445   3777
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.94 %
    Favored  : 98.95 %
  Cbeta Deviations :  0.56 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.26 (0.24), residues: 1172
  helix:  1.29 (0.18), residues: 791
  sheet:  0.48 (0.63), residues: 70
  loop : -0.05 (0.36), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 954 
 TYR   0.023   0.002   TYR A 958 
 PHE   0.041   0.002   PHE A 974 
 TRP   0.011   0.001   TRP A 228 
 HIS   0.008   0.001   HIS A 932 

Details of bonding type rmsd
  covalent geometry    : bond        0.00611 ( 9518)
  covalent geometry    : angle       0.86108 (12913)
  hydrogen bonds       : bond        0.15384 (  631)
  hydrogen bonds       : angle       6.14853 ( 1851)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 145
  time to evaluate  : 0.293 
Fit side-chains
REVERT: A  312 TYR cc_start: 0.7271 (t80) cc_final: 0.7051 (t80)
REVERT: A  404 GLN cc_start: 0.8021 (mt0) cc_final: 0.7625 (mm-40)
REVERT: A  612 MET cc_start: 0.5970 (mmt) cc_final: 0.5493 (mpp)
REVERT: A 1057 LYS cc_start: 0.7814 (mttt) cc_final: 0.7292 (mptt)
REVERT: A 1152 GLN cc_start: 0.7339 (mt0) cc_final: 0.7048 (mp-120)
REVERT: A 1208 LYS cc_start: 0.7472 (tttm) cc_final: 0.7196 (ttpt)
REVERT: A 1216 LYS cc_start: 0.7381 (ttmm) cc_final: 0.6986 (mttp)
  outliers start: 1
  outliers final: 0
  residues processed: 146
  average time/residue: 0.7351
  time to fit residues: 113.1228
Evaluate side-chains
  118 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 108 optimal weight:    0.5980
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    0.8980
   chunk 113 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    6.9990
   chunk 100 optimal weight:    4.9990
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
A 343 GLN
A 452 GLN
** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1030 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.178986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.126880 restraints weight = 8688.353|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 1.68
r_work: 0.3252 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3106 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.1499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   9518  Z= 0.216
  Angle     :  0.631   9.221  12913  Z= 0.329
  Chirality :  0.044   0.150   1490
  Planarity :  0.004   0.035   1606
  Dihedral  : 11.631  88.044   1685
  Min Nonbonded Distance : 1.891

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  :  9.86 %
    Favored  : 88.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.29 (0.24), residues: 1172
  helix:  1.31 (0.18), residues: 799
  sheet:  0.51 (0.65), residues: 70
  loop : -0.08 (0.35), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 400 
 TYR   0.015   0.002   TYR A 506 
 PHE   0.028   0.002   PHE A 332 
 TRP   0.010   0.002   TRP A 228 
 HIS   0.005   0.001   HIS A  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00493 ( 9518)
  covalent geometry    : angle       0.63134 (12913)
  hydrogen bonds       : bond        0.06128 (  631)
  hydrogen bonds       : angle       4.48488 ( 1851)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 129
  time to evaluate  : 0.391 
Fit side-chains
REVERT: A  112 TYR cc_start: 0.7005 (m-80) cc_final: 0.6664 (m-80)
REVERT: A  312 TYR cc_start: 0.7033 (t80) cc_final: 0.6591 (t80)
REVERT: A  402 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7406 (mt-10)
REVERT: A  404 GLN cc_start: 0.8338 (mt0) cc_final: 0.7257 (mm-40)
REVERT: A  592 ASP cc_start: 0.7367 (m-30) cc_final: 0.7099 (m-30)
REVERT: A  728 PHE cc_start: 0.6893 (t80) cc_final: 0.6505 (t80)
REVERT: A  753 LEU cc_start: 0.7235 (tt) cc_final: 0.6762 (tm)
REVERT: A  872 MET cc_start: 0.6628 (OUTLIER) cc_final: 0.5403 (ttm)
REVERT: A  918 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7404 (tm-30)
REVERT: A  930 LYS cc_start: 0.8062 (ttpt) cc_final: 0.7803 (tttt)
REVERT: A 1057 LYS cc_start: 0.6833 (mttt) cc_final: 0.5756 (mptt)
REVERT: A 1096 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7271 (tt0)
REVERT: A 1152 GLN cc_start: 0.7888 (mt0) cc_final: 0.6690 (mp-120)
REVERT: A 1189 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.8063 (mt0)
REVERT: A 1208 LYS cc_start: 0.6779 (tttm) cc_final: 0.6107 (ttpt)
REVERT: A 1215 ASP cc_start: 0.7068 (m-30) cc_final: 0.6715 (m-30)
REVERT: A 1216 LYS cc_start: 0.7098 (ttmm) cc_final: 0.6411 (mttp)
  outliers start: 20
  outliers final: 4
  residues processed: 136
  average time/residue: 0.6700
  time to fit residues: 96.5942
Evaluate side-chains
  129 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 120
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  402 GLU
Chi-restraints excluded: chain A residue  444 ASP
Chi-restraints excluded: chain A residue  814 LEU
Chi-restraints excluded: chain A residue  872 MET
Chi-restraints excluded: chain A residue  881 LYS
Chi-restraints excluded: chain A residue  918 GLN
Chi-restraints excluded: chain A residue 1096 GLU
Chi-restraints excluded: chain A residue 1189 GLN
Chi-restraints excluded: chain A residue 1203 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 52 optimal weight:    5.9990
   chunk 25 optimal weight:    0.7980
   chunk 91 optimal weight:    3.9990
   chunk 97 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 78 optimal weight:    0.8980
   chunk 38 optimal weight:    4.9990
   chunk 45 optimal weight:    0.7980
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A 452 GLN
** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1030 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.181205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.129285 restraints weight = 8647.751|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 1.69
r_work: 0.3283 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3138 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.1684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   9518  Z= 0.139
  Angle     :  0.542   8.689  12913  Z= 0.280
  Chirality :  0.040   0.145   1490
  Planarity :  0.003   0.032   1606
  Dihedral  : 11.038  86.729   1685
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.88 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 12.28 %
    Favored  : 85.10 %
  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 are not related in a simple way.
  whole:  1.49 (0.24), residues: 1172
  helix:  1.52 (0.18), residues: 801
  sheet:  0.47 (0.63), residues: 70
  loop : -0.19 (0.35), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 954 
 TYR   0.010   0.001   TYR A 849 
 PHE   0.024   0.002   PHE A 332 
 TRP   0.012   0.001   TRP A 228 
 HIS   0.005   0.001   HIS A1003 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 9518)
  covalent geometry    : angle       0.54162 (12913)
  hydrogen bonds       : bond        0.05210 (  631)
  hydrogen bonds       : angle       4.18689 ( 1851)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 134
  time to evaluate  : 0.327 
Fit side-chains
REVERT: A  112 TYR cc_start: 0.6974 (m-80) cc_final: 0.6695 (m-80)
REVERT: A  204 PHE cc_start: 0.7666 (OUTLIER) cc_final: 0.7439 (m-80)
REVERT: A  221 LEU cc_start: 0.6806 (OUTLIER) cc_final: 0.6296 (mp)
REVERT: A  312 TYR cc_start: 0.7039 (t80) cc_final: 0.6589 (t80)
REVERT: A  402 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7393 (mt-10)
REVERT: A  404 GLN cc_start: 0.8342 (mt0) cc_final: 0.7252 (mm-40)
REVERT: A  592 ASP cc_start: 0.7312 (m-30) cc_final: 0.7018 (m-30)
REVERT: A  612 MET cc_start: 0.5479 (mmm) cc_final: 0.4663 (mmm)
REVERT: A  753 LEU cc_start: 0.7385 (tt) cc_final: 0.6835 (tm)
REVERT: A  872 MET cc_start: 0.6481 (OUTLIER) cc_final: 0.5254 (mtm)
REVERT: A  918 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7346 (tm-30)
REVERT: A  928 MET cc_start: 0.8773 (mmp) cc_final: 0.8435 (mmp)
REVERT: A  930 LYS cc_start: 0.8179 (ttpt) cc_final: 0.7858 (tttt)
REVERT: A 1057 LYS cc_start: 0.6815 (mttt) cc_final: 0.5726 (mptt)
REVERT: A 1096 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7201 (tt0)
REVERT: A 1152 GLN cc_start: 0.7891 (mt0) cc_final: 0.6677 (mp-120)
REVERT: A 1208 LYS cc_start: 0.6737 (tttm) cc_final: 0.6057 (ttpt)
REVERT: A 1215 ASP cc_start: 0.7081 (m-30) cc_final: 0.6839 (m-30)
  outliers start: 25
  outliers final: 5
  residues processed: 146
  average time/residue: 0.6688
  time to fit residues: 103.5556
Evaluate side-chains
  131 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 120
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  402 GLU
Chi-restraints excluded: chain A residue  444 ASP
Chi-restraints excluded: chain A residue  470 SER
Chi-restraints excluded: chain A residue  864 ILE
Chi-restraints excluded: chain A residue  872 MET
Chi-restraints excluded: chain A residue  881 LYS
Chi-restraints excluded: chain A residue  918 GLN
Chi-restraints excluded: chain A residue 1096 GLU
Chi-restraints excluded: chain A residue 1203 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 72 optimal weight:    0.9980
   chunk 74 optimal weight:    8.9990
   chunk 12 optimal weight:    0.9990
   chunk 111 optimal weight:    4.9990
   chunk 98 optimal weight:    0.9990
   chunk 104 optimal weight:    3.9990
   chunk 35 optimal weight:    0.0980
   chunk 51 optimal weight:    0.0270
   chunk 46 optimal weight:    0.7980
   chunk 75 optimal weight:    3.9990
   chunk 89 optimal weight:    0.9990
   overall best weight:    0.5840

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
A 392 ASN
A 452 GLN
** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 878 GLN
A1003 HIS
A1030 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.182274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.130596 restraints weight = 8719.856|
|-----------------------------------------------------------------------------|
r_work (start): 0.3461 rms_B_bonded: 1.68
r_work: 0.3315 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3171 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.1890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   9518  Z= 0.120
  Angle     :  0.499   7.782  12913  Z= 0.261
  Chirality :  0.039   0.174   1490
  Planarity :  0.003   0.032   1606
  Dihedral  : 10.180  86.184   1685
  Min Nonbonded Distance : 1.999

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.88 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 12.70 %
    Favored  : 84.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.74 (0.24), residues: 1172
  helix:  1.73 (0.18), residues: 800
  sheet:  0.56 (0.63), residues: 70
  loop : -0.16 (0.35), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 954 
 TYR   0.010   0.001   TYR A 849 
 PHE   0.024   0.001   PHE A 332 
 TRP   0.012   0.001   TRP A 228 
 HIS   0.003   0.001   HIS A1003 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 9518)
  covalent geometry    : angle       0.49896 (12913)
  hydrogen bonds       : bond        0.04752 (  631)
  hydrogen bonds       : angle       4.00405 ( 1851)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 130
  time to evaluate  : 0.344 
Fit side-chains
REVERT: A  112 TYR cc_start: 0.6983 (m-80) cc_final: 0.6697 (m-80)
REVERT: A  114 TYR cc_start: 0.7700 (m-80) cc_final: 0.7440 (m-80)
REVERT: A  204 PHE cc_start: 0.7607 (OUTLIER) cc_final: 0.7193 (m-80)
REVERT: A  221 LEU cc_start: 0.6814 (OUTLIER) cc_final: 0.6271 (mp)
REVERT: A  312 TYR cc_start: 0.7063 (t80) cc_final: 0.6575 (t80)
REVERT: A  402 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7358 (mt-10)
REVERT: A  404 GLN cc_start: 0.8347 (mt0) cc_final: 0.7256 (mm-40)
REVERT: A  444 ASP cc_start: 0.8043 (OUTLIER) cc_final: 0.7833 (t70)
REVERT: A  592 ASP cc_start: 0.7268 (m-30) cc_final: 0.6982 (m-30)
REVERT: A  612 MET cc_start: 0.5636 (mmm) cc_final: 0.4931 (mmm)
REVERT: A  725 SER cc_start: 0.7909 (t) cc_final: 0.7635 (p)
REVERT: A  753 LEU cc_start: 0.7349 (tt) cc_final: 0.6798 (tm)
REVERT: A  872 MET cc_start: 0.6348 (OUTLIER) cc_final: 0.5295 (mtm)
REVERT: A  918 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7309 (tm-30)
REVERT: A  930 LYS cc_start: 0.8198 (ttpt) cc_final: 0.7855 (tttt)
REVERT: A  953 PHE cc_start: 0.7759 (OUTLIER) cc_final: 0.6939 (t80)
REVERT: A 1057 LYS cc_start: 0.6814 (mttt) cc_final: 0.5740 (mptt)
REVERT: A 1096 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7195 (tt0)
REVERT: A 1152 GLN cc_start: 0.7915 (mt0) cc_final: 0.6704 (mp-120)
REVERT: A 1208 LYS cc_start: 0.6832 (tttm) cc_final: 0.6108 (ttpt)
REVERT: A 1215 ASP cc_start: 0.7083 (OUTLIER) cc_final: 0.6848 (m-30)
REVERT: A 1246 LYS cc_start: 0.7317 (OUTLIER) cc_final: 0.6214 (mmtm)
  outliers start: 29
  outliers final: 2
  residues processed: 137
  average time/residue: 0.6884
  time to fit residues: 99.7716
Evaluate side-chains
  136 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 124
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  314 THR
Chi-restraints excluded: chain A residue  402 GLU
Chi-restraints excluded: chain A residue  444 ASP
Chi-restraints excluded: chain A residue  872 MET
Chi-restraints excluded: chain A residue  918 GLN
Chi-restraints excluded: chain A residue  953 PHE
Chi-restraints excluded: chain A residue 1096 GLU
Chi-restraints excluded: chain A residue 1215 ASP
Chi-restraints excluded: chain A residue 1246 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 90 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 114 optimal weight:   10.0000
   chunk 35 optimal weight:    0.1980
   chunk 83 optimal weight:    3.9990
   chunk 23 optimal weight:    0.8980
   chunk 59 optimal weight:    6.9990
   chunk 63 optimal weight:    0.9990
   chunk 38 optimal weight:    5.9990
   overall best weight:    0.8186

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

Flipped N/Q/H residues before XYZ refinement:
A 452 GLN
** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 820 GLN
A1030 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.181477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.129772 restraints weight = 8715.633|
|-----------------------------------------------------------------------------|
r_work (start): 0.3450 rms_B_bonded: 1.68
r_work: 0.3303 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3160 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.1992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   9518  Z= 0.129
  Angle     :  0.499   7.775  12913  Z= 0.262
  Chirality :  0.039   0.170   1490
  Planarity :  0.003   0.031   1606
  Dihedral  : 10.028  85.792   1685
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.96 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 13.75 %
    Favored  : 83.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.75 (0.24), residues: 1172
  helix:  1.75 (0.18), residues: 800
  sheet:  0.58 (0.63), residues: 70
  loop : -0.19 (0.35), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 954 
 TYR   0.010   0.001   TYR A 849 
 PHE   0.022   0.002   PHE A 332 
 TRP   0.011   0.001   TRP A 228 
 HIS   0.003   0.001   HIS A1151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 9518)
  covalent geometry    : angle       0.49899 (12913)
  hydrogen bonds       : bond        0.04825 (  631)
  hydrogen bonds       : angle       3.96825 ( 1851)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 127
  time to evaluate  : 0.286 
Fit side-chains
REVERT: A  112 TYR cc_start: 0.6976 (m-80) cc_final: 0.6731 (m-80)
REVERT: A  114 TYR cc_start: 0.7716 (m-80) cc_final: 0.7216 (m-80)
REVERT: A  204 PHE cc_start: 0.7609 (OUTLIER) cc_final: 0.7135 (m-80)
REVERT: A  221 LEU cc_start: 0.6811 (OUTLIER) cc_final: 0.6250 (mp)
REVERT: A  312 TYR cc_start: 0.7058 (t80) cc_final: 0.6578 (t80)
REVERT: A  402 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7375 (mt-10)
REVERT: A  404 GLN cc_start: 0.8370 (mt0) cc_final: 0.7269 (mm-40)
REVERT: A  444 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7844 (t70)
REVERT: A  592 ASP cc_start: 0.7280 (m-30) cc_final: 0.6993 (m-30)
REVERT: A  612 MET cc_start: 0.5650 (mmm) cc_final: 0.4929 (mmm)
REVERT: A  753 LEU cc_start: 0.7334 (tt) cc_final: 0.6778 (tm)
REVERT: A  846 SER cc_start: 0.6804 (m) cc_final: 0.6604 (p)
REVERT: A  872 MET cc_start: 0.6388 (OUTLIER) cc_final: 0.5343 (mtm)
REVERT: A  918 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7322 (tm-30)
REVERT: A  930 LYS cc_start: 0.8229 (ttpt) cc_final: 0.7870 (tttt)
REVERT: A  953 PHE cc_start: 0.7786 (OUTLIER) cc_final: 0.7025 (t80)
REVERT: A  961 THR cc_start: 0.7117 (OUTLIER) cc_final: 0.6506 (p)
REVERT: A 1057 LYS cc_start: 0.6802 (mttt) cc_final: 0.5735 (mptt)
REVERT: A 1152 GLN cc_start: 0.7906 (mt0) cc_final: 0.6692 (mp-120)
REVERT: A 1215 ASP cc_start: 0.7078 (m-30) cc_final: 0.6816 (m-30)
  outliers start: 27
  outliers final: 6
  residues processed: 139
  average time/residue: 0.6424
  time to fit residues: 94.7139
Evaluate side-chains
  133 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 119
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  314 THR
Chi-restraints excluded: chain A residue  402 GLU
Chi-restraints excluded: chain A residue  444 ASP
Chi-restraints excluded: chain A residue  470 SER
Chi-restraints excluded: chain A residue  814 LEU
Chi-restraints excluded: chain A residue  872 MET
Chi-restraints excluded: chain A residue  918 GLN
Chi-restraints excluded: chain A residue  953 PHE
Chi-restraints excluded: chain A residue  961 THR
Chi-restraints excluded: chain A residue 1203 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 75 optimal weight:    7.9990
   chunk 15 optimal weight:    0.7980
   chunk 58 optimal weight:    0.1980
   chunk 109 optimal weight:    0.9980
   chunk 25 optimal weight:    0.7980
   chunk 32 optimal weight:    0.8980
   chunk 77 optimal weight:    3.9990
   chunk 29 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9990
   chunk 30 optimal weight:   10.0000
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 452 GLN
** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1030 ASN
A1099 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.181923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.130221 restraints weight = 8728.397|
|-----------------------------------------------------------------------------|
r_work (start): 0.3457 rms_B_bonded: 1.68
r_work: 0.3312 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3170 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.2110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   9518  Z= 0.121
  Angle     :  0.486   7.219  12913  Z= 0.257
  Chirality :  0.039   0.184   1490
  Planarity :  0.003   0.031   1606
  Dihedral  :  9.851  84.689   1685
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.96 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 14.17 %
    Favored  : 82.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.83 (0.24), residues: 1172
  helix:  1.83 (0.18), residues: 800
  sheet:  0.55 (0.63), residues: 70
  loop : -0.18 (0.35), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 785 
 TYR   0.020   0.001   TYR A 506 
 PHE   0.019   0.001   PHE A 508 
 TRP   0.012   0.001   TRP A 228 
 HIS   0.002   0.001   HIS A 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 9518)
  covalent geometry    : angle       0.48562 (12913)
  hydrogen bonds       : bond        0.04679 (  631)
  hydrogen bonds       : angle       3.90748 ( 1851)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 127
  time to evaluate  : 0.293 
Fit side-chains
REVERT: A  112 TYR cc_start: 0.6984 (m-80) cc_final: 0.6765 (m-80)
REVERT: A  114 TYR cc_start: 0.7736 (m-80) cc_final: 0.7250 (m-80)
REVERT: A  204 PHE cc_start: 0.7681 (OUTLIER) cc_final: 0.7184 (m-80)
REVERT: A  221 LEU cc_start: 0.6849 (OUTLIER) cc_final: 0.6277 (mp)
REVERT: A  312 TYR cc_start: 0.7082 (t80) cc_final: 0.6605 (t80)
REVERT: A  402 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7336 (mt-10)
REVERT: A  566 GLN cc_start: 0.6941 (tp40) cc_final: 0.6655 (mm110)
REVERT: A  592 ASP cc_start: 0.7291 (m-30) cc_final: 0.6998 (m-30)
REVERT: A  612 MET cc_start: 0.5630 (mmm) cc_final: 0.4900 (mmm)
REVERT: A  753 LEU cc_start: 0.7364 (tt) cc_final: 0.6789 (tm)
REVERT: A  846 SER cc_start: 0.6824 (m) cc_final: 0.6611 (p)
REVERT: A  872 MET cc_start: 0.6463 (OUTLIER) cc_final: 0.5509 (mtm)
REVERT: A  928 MET cc_start: 0.8708 (mmp) cc_final: 0.8505 (mmp)
REVERT: A  929 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7981 (ttmt)
REVERT: A  930 LYS cc_start: 0.8250 (ttpt) cc_final: 0.7879 (tttt)
REVERT: A  953 PHE cc_start: 0.7824 (OUTLIER) cc_final: 0.7039 (t80)
REVERT: A  961 THR cc_start: 0.7131 (OUTLIER) cc_final: 0.6540 (p)
REVERT: A  968 GLU cc_start: 0.7348 (mp0) cc_final: 0.6521 (mt-10)
REVERT: A 1030 ASN cc_start: 0.8238 (m-40) cc_final: 0.7705 (m-40)
REVERT: A 1057 LYS cc_start: 0.6821 (mttt) cc_final: 0.5768 (mptt)
REVERT: A 1152 GLN cc_start: 0.7916 (mt0) cc_final: 0.6710 (mp-120)
REVERT: A 1215 ASP cc_start: 0.7074 (OUTLIER) cc_final: 0.6797 (m-30)
REVERT: A 1246 LYS cc_start: 0.7391 (mttp) cc_final: 0.6313 (mmtm)
  outliers start: 29
  outliers final: 7
  residues processed: 140
  average time/residue: 0.6708
  time to fit residues: 99.5694
Evaluate side-chains
  137 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 122
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 MET
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  314 THR
Chi-restraints excluded: chain A residue  402 GLU
Chi-restraints excluded: chain A residue  470 SER
Chi-restraints excluded: chain A residue  729 SER
Chi-restraints excluded: chain A residue  872 MET
Chi-restraints excluded: chain A residue  929 LYS
Chi-restraints excluded: chain A residue  953 PHE
Chi-restraints excluded: chain A residue  961 THR
Chi-restraints excluded: chain A residue 1203 ASP
Chi-restraints excluded: chain A residue 1215 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 98 optimal weight:    3.9990
   chunk 46 optimal weight:    0.7980
   chunk 94 optimal weight:    1.9990
   chunk 95 optimal weight:    0.0470
   chunk 30 optimal weight:    0.7980
   chunk 114 optimal weight:    5.9990
   chunk 79 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9980
   overall best weight:    0.7278

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

Flipped N/Q/H residues before XYZ refinement:
A 452 GLN
** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.181584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.129673 restraints weight = 8756.585|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 1.69
r_work: 0.3306 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3163 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.2191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   9518  Z= 0.122
  Angle     :  0.487   7.360  12913  Z= 0.257
  Chirality :  0.039   0.199   1490
  Planarity :  0.003   0.032   1606
  Dihedral  :  9.801  84.790   1685
  Min Nonbonded Distance : 1.966

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.22 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 15.32 %
    Favored  : 82.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.87 (0.24), residues: 1172
  helix:  1.84 (0.18), residues: 800
  sheet:  0.58 (0.63), residues: 70
  loop : -0.15 (0.35), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1106 
 TYR   0.010   0.001   TYR A 849 
 PHE   0.017   0.001   PHE A 508 
 TRP   0.011   0.001   TRP A 228 
 HIS   0.002   0.001   HIS A 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 9518)
  covalent geometry    : angle       0.48669 (12913)
  hydrogen bonds       : bond        0.04651 (  631)
  hydrogen bonds       : angle       3.88818 ( 1851)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 127
  time to evaluate  : 0.322 
Fit side-chains
REVERT: A  112 TYR cc_start: 0.7098 (m-80) cc_final: 0.6867 (m-80)
REVERT: A  114 TYR cc_start: 0.7660 (m-80) cc_final: 0.7128 (m-80)
REVERT: A  204 PHE cc_start: 0.7642 (OUTLIER) cc_final: 0.7243 (m-80)
REVERT: A  221 LEU cc_start: 0.6844 (OUTLIER) cc_final: 0.6281 (mp)
REVERT: A  312 TYR cc_start: 0.7038 (t80) cc_final: 0.6569 (t80)
REVERT: A  402 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7343 (mt-10)
REVERT: A  566 GLN cc_start: 0.6964 (tp40) cc_final: 0.6697 (mm110)
REVERT: A  592 ASP cc_start: 0.7271 (m-30) cc_final: 0.6975 (m-30)
REVERT: A  612 MET cc_start: 0.5630 (mmm) cc_final: 0.4902 (mmm)
REVERT: A  753 LEU cc_start: 0.7318 (tt) cc_final: 0.6765 (tm)
REVERT: A  846 SER cc_start: 0.6837 (m) cc_final: 0.6607 (p)
REVERT: A  872 MET cc_start: 0.6586 (OUTLIER) cc_final: 0.5654 (mtm)
REVERT: A  918 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7282 (tm-30)
REVERT: A  930 LYS cc_start: 0.8211 (ttpt) cc_final: 0.7833 (tttt)
REVERT: A  953 PHE cc_start: 0.7787 (OUTLIER) cc_final: 0.6964 (t80)
REVERT: A  961 THR cc_start: 0.7102 (OUTLIER) cc_final: 0.6515 (p)
REVERT: A  968 GLU cc_start: 0.7337 (mp0) cc_final: 0.6525 (mt-10)
REVERT: A 1057 LYS cc_start: 0.6857 (mttt) cc_final: 0.5773 (mptt)
REVERT: A 1152 GLN cc_start: 0.7910 (mt0) cc_final: 0.6706 (mp-120)
REVERT: A 1215 ASP cc_start: 0.7069 (OUTLIER) cc_final: 0.6809 (m-30)
REVERT: A 1243 GLN cc_start: 0.6635 (mm-40) cc_final: 0.6386 (mt0)
REVERT: A 1246 LYS cc_start: 0.7421 (mttp) cc_final: 0.6372 (mmtm)
  outliers start: 25
  outliers final: 8
  residues processed: 137
  average time/residue: 0.6548
  time to fit residues: 95.0479
Evaluate side-chains
  136 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 120
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 MET
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  314 THR
Chi-restraints excluded: chain A residue  402 GLU
Chi-restraints excluded: chain A residue  470 SER
Chi-restraints excluded: chain A residue  757 ILE
Chi-restraints excluded: chain A residue  872 MET
Chi-restraints excluded: chain A residue  895 GLU
Chi-restraints excluded: chain A residue  918 GLN
Chi-restraints excluded: chain A residue  953 PHE
Chi-restraints excluded: chain A residue  961 THR
Chi-restraints excluded: chain A residue 1203 ASP
Chi-restraints excluded: chain A residue 1215 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 33 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 100 optimal weight:    6.9990
   chunk 24 optimal weight:    0.5980
   chunk 32 optimal weight:    0.6980
   chunk 48 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 26 optimal weight:    0.6980
   chunk 75 optimal weight:    3.9990
   chunk 94 optimal weight:    0.8980
   chunk 66 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 452 GLN
** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1030 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.181651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.129831 restraints weight = 8691.687|
|-----------------------------------------------------------------------------|
r_work (start): 0.3452 rms_B_bonded: 1.69
r_work: 0.3306 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3164 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.2259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   9518  Z= 0.121
  Angle     :  0.485   7.198  12913  Z= 0.256
  Chirality :  0.039   0.196   1490
  Planarity :  0.003   0.031   1606
  Dihedral  :  9.735  84.072   1685
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.05 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 15.84 %
    Favored  : 81.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.82 (0.24), residues: 1172
  helix:  1.83 (0.18), residues: 805
  sheet:  0.54 (0.63), residues: 70
  loop : -0.27 (0.35), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 954 
 TYR   0.015   0.001   TYR A 506 
 PHE   0.019   0.001   PHE A 332 
 TRP   0.011   0.001   TRP A 228 
 HIS   0.002   0.001   HIS A 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 9518)
  covalent geometry    : angle       0.48502 (12913)
  hydrogen bonds       : bond        0.04609 (  631)
  hydrogen bonds       : angle       3.86407 ( 1851)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 122
  time to evaluate  : 0.342 
Fit side-chains
REVERT: A  112 TYR cc_start: 0.7081 (m-80) cc_final: 0.6881 (m-80)
REVERT: A  114 TYR cc_start: 0.7617 (m-80) cc_final: 0.7058 (m-80)
REVERT: A  204 PHE cc_start: 0.7657 (OUTLIER) cc_final: 0.7206 (m-80)
REVERT: A  221 LEU cc_start: 0.6829 (OUTLIER) cc_final: 0.6266 (mp)
REVERT: A  312 TYR cc_start: 0.7043 (t80) cc_final: 0.6558 (t80)
REVERT: A  402 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7336 (mt-10)
REVERT: A  470 SER cc_start: 0.7596 (OUTLIER) cc_final: 0.7378 (t)
REVERT: A  566 GLN cc_start: 0.6948 (tp40) cc_final: 0.6690 (mm110)
REVERT: A  592 ASP cc_start: 0.7261 (m-30) cc_final: 0.6982 (m-30)
REVERT: A  612 MET cc_start: 0.5648 (mmm) cc_final: 0.4916 (mmm)
REVERT: A  753 LEU cc_start: 0.7314 (tt) cc_final: 0.6745 (tm)
REVERT: A  846 SER cc_start: 0.6827 (m) cc_final: 0.6598 (p)
REVERT: A  872 MET cc_start: 0.6576 (OUTLIER) cc_final: 0.5667 (mtm)
REVERT: A  918 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7283 (tm-30)
REVERT: A  930 LYS cc_start: 0.8195 (ttpt) cc_final: 0.7825 (tttt)
REVERT: A  953 PHE cc_start: 0.7767 (OUTLIER) cc_final: 0.6919 (t80)
REVERT: A  961 THR cc_start: 0.7121 (OUTLIER) cc_final: 0.6541 (p)
REVERT: A  968 GLU cc_start: 0.7303 (mp0) cc_final: 0.6473 (mt-10)
REVERT: A 1030 ASN cc_start: 0.8310 (m-40) cc_final: 0.7783 (m-40)
REVERT: A 1057 LYS cc_start: 0.6834 (mttt) cc_final: 0.5775 (mptt)
REVERT: A 1152 GLN cc_start: 0.7909 (mt0) cc_final: 0.6704 (mp-120)
REVERT: A 1215 ASP cc_start: 0.7049 (OUTLIER) cc_final: 0.6775 (m-30)
REVERT: A 1243 GLN cc_start: 0.6627 (mm-40) cc_final: 0.6392 (mt0)
REVERT: A 1246 LYS cc_start: 0.7408 (mttp) cc_final: 0.6344 (mmtm)
  outliers start: 22
  outliers final: 7
  residues processed: 130
  average time/residue: 0.6324
  time to fit residues: 87.4095
Evaluate side-chains
  136 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 120
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 MET
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  314 THR
Chi-restraints excluded: chain A residue  402 GLU
Chi-restraints excluded: chain A residue  470 SER
Chi-restraints excluded: chain A residue  814 LEU
Chi-restraints excluded: chain A residue  872 MET
Chi-restraints excluded: chain A residue  918 GLN
Chi-restraints excluded: chain A residue  953 PHE
Chi-restraints excluded: chain A residue  954 ARG
Chi-restraints excluded: chain A residue  961 THR
Chi-restraints excluded: chain A residue 1203 ASP
Chi-restraints excluded: chain A residue 1215 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 68 optimal weight:    2.9990
   chunk 113 optimal weight:    4.9990
   chunk 88 optimal weight:    4.9990
   chunk 81 optimal weight:    1.9990
   chunk 92 optimal weight:    5.9990
   chunk 36 optimal weight:    0.6980
   chunk 8 optimal weight:    0.8980
   chunk 72 optimal weight:    0.9980
   chunk 5 optimal weight:    0.0370
   chunk 80 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.9260

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

Flipped N/Q/H residues before XYZ refinement:
A 452 GLN
** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.180576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.128484 restraints weight = 8686.034|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 1.69
r_work: 0.3291 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3148 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.2271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9518  Z= 0.133
  Angle     :  0.499   7.570  12913  Z= 0.263
  Chirality :  0.039   0.202   1490
  Planarity :  0.003   0.031   1606
  Dihedral  :  9.758  84.234   1685
  Min Nonbonded Distance : 1.947

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.22 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 16.16 %
    Favored  : 81.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.73 (0.24), residues: 1172
  helix:  1.75 (0.18), residues: 806
  sheet:  0.53 (0.63), residues: 70
  loop : -0.25 (0.35), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 954 
 TYR   0.010   0.001   TYR A 849 
 PHE   0.020   0.001   PHE A 508 
 TRP   0.011   0.001   TRP A 228 
 HIS   0.003   0.001   HIS A1151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 9518)
  covalent geometry    : angle       0.49941 (12913)
  hydrogen bonds       : bond        0.04793 (  631)
  hydrogen bonds       : angle       3.90522 ( 1851)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 124
  time to evaluate  : 0.228 
Fit side-chains
REVERT: A  112 TYR cc_start: 0.7092 (m-80) cc_final: 0.6876 (m-80)
REVERT: A  114 TYR cc_start: 0.7622 (m-80) cc_final: 0.7012 (m-80)
REVERT: A  204 PHE cc_start: 0.7647 (OUTLIER) cc_final: 0.7257 (m-80)
REVERT: A  221 LEU cc_start: 0.6859 (OUTLIER) cc_final: 0.6292 (mp)
REVERT: A  312 TYR cc_start: 0.7033 (t80) cc_final: 0.6563 (t80)
REVERT: A  402 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7341 (mt-10)
REVERT: A  404 GLN cc_start: 0.8392 (mt0) cc_final: 0.7287 (mm-40)
REVERT: A  470 SER cc_start: 0.7630 (OUTLIER) cc_final: 0.7415 (t)
REVERT: A  566 GLN cc_start: 0.6963 (tp40) cc_final: 0.6665 (mm110)
REVERT: A  592 ASP cc_start: 0.7259 (m-30) cc_final: 0.6979 (m-30)
REVERT: A  612 MET cc_start: 0.5595 (mmm) cc_final: 0.4875 (mmm)
REVERT: A  753 LEU cc_start: 0.7304 (tt) cc_final: 0.6747 (tm)
REVERT: A  804 LYS cc_start: 0.8174 (mtpp) cc_final: 0.7748 (mttm)
REVERT: A  846 SER cc_start: 0.6836 (m) cc_final: 0.6598 (p)
REVERT: A  872 MET cc_start: 0.6629 (OUTLIER) cc_final: 0.5680 (mtm)
REVERT: A  918 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7308 (tm-30)
REVERT: A  929 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7954 (ttmt)
REVERT: A  953 PHE cc_start: 0.7779 (OUTLIER) cc_final: 0.6895 (t80)
REVERT: A  968 GLU cc_start: 0.7285 (mp0) cc_final: 0.6464 (mt-10)
REVERT: A 1030 ASN cc_start: 0.8318 (m-40) cc_final: 0.7847 (m-40)
REVERT: A 1057 LYS cc_start: 0.6839 (mttt) cc_final: 0.5777 (mptt)
REVERT: A 1152 GLN cc_start: 0.7896 (mt0) cc_final: 0.6683 (mp-120)
REVERT: A 1215 ASP cc_start: 0.7078 (OUTLIER) cc_final: 0.6803 (m-30)
REVERT: A 1243 GLN cc_start: 0.6660 (mm-40) cc_final: 0.6418 (mt0)
REVERT: A 1246 LYS cc_start: 0.7451 (mttp) cc_final: 0.6380 (mmtm)
  outliers start: 19
  outliers final: 7
  residues processed: 131
  average time/residue: 0.6790
  time to fit residues: 94.1876
Evaluate side-chains
  136 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 120
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 MET
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  314 THR
Chi-restraints excluded: chain A residue  402 GLU
Chi-restraints excluded: chain A residue  470 SER
Chi-restraints excluded: chain A residue  814 LEU
Chi-restraints excluded: chain A residue  872 MET
Chi-restraints excluded: chain A residue  895 GLU
Chi-restraints excluded: chain A residue  918 GLN
Chi-restraints excluded: chain A residue  929 LYS
Chi-restraints excluded: chain A residue  953 PHE
Chi-restraints excluded: chain A residue 1203 ASP
Chi-restraints excluded: chain A residue 1215 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 8 optimal weight:    0.4980
   chunk 55 optimal weight:    7.9990
   chunk 4 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 87 optimal weight:    6.9990
   chunk 113 optimal weight:    3.9990
   chunk 16 optimal weight:    4.9990
   chunk 83 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 94 optimal weight:    0.9990
   overall best weight:    1.0586

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

Flipped N/Q/H residues before XYZ refinement:
A 452 GLN
** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.180189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.128162 restraints weight = 8653.634|
|-----------------------------------------------------------------------------|
r_work (start): 0.3429 rms_B_bonded: 1.67
r_work: 0.3282 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3140 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.2312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   9518  Z= 0.141
  Angle     :  0.511   8.287  12913  Z= 0.268
  Chirality :  0.040   0.197   1490
  Planarity :  0.003   0.031   1606
  Dihedral  :  9.760  83.662   1685
  Min Nonbonded Distance : 1.940

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.13 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 16.89 %
    Favored  : 81.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.69 (0.24), residues: 1172
  helix:  1.71 (0.18), residues: 804
  sheet:  0.50 (0.64), residues: 70
  loop : -0.27 (0.34), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 954 
 TYR   0.017   0.001   TYR A 506 
 PHE   0.024   0.002   PHE A 332 
 TRP   0.010   0.001   TRP A 228 
 HIS   0.003   0.001   HIS A1151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 9518)
  covalent geometry    : angle       0.51114 (12913)
  hydrogen bonds       : bond        0.04906 (  631)
  hydrogen bonds       : angle       3.94527 ( 1851)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 123
  time to evaluate  : 0.352 
Fit side-chains
REVERT: A  112 TYR cc_start: 0.7119 (m-80) cc_final: 0.6896 (m-80)
REVERT: A  114 TYR cc_start: 0.7626 (m-80) cc_final: 0.7039 (m-80)
REVERT: A  204 PHE cc_start: 0.7669 (OUTLIER) cc_final: 0.7261 (m-80)
REVERT: A  221 LEU cc_start: 0.6820 (OUTLIER) cc_final: 0.6253 (mp)
REVERT: A  312 TYR cc_start: 0.7014 (t80) cc_final: 0.6527 (t80)
REVERT: A  402 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7392 (mt-10)
REVERT: A  404 GLN cc_start: 0.8389 (mt0) cc_final: 0.7288 (mm-40)
REVERT: A  566 GLN cc_start: 0.6923 (tp40) cc_final: 0.6641 (mm110)
REVERT: A  592 ASP cc_start: 0.7292 (m-30) cc_final: 0.7008 (m-30)
REVERT: A  612 MET cc_start: 0.5660 (mmm) cc_final: 0.4939 (mmm)
REVERT: A  753 LEU cc_start: 0.7291 (tt) cc_final: 0.6746 (tm)
REVERT: A  804 LYS cc_start: 0.8192 (mtpp) cc_final: 0.7760 (mttm)
REVERT: A  846 SER cc_start: 0.6853 (m) cc_final: 0.6605 (p)
REVERT: A  872 MET cc_start: 0.6544 (OUTLIER) cc_final: 0.5578 (mtm)
REVERT: A  918 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7307 (tm-30)
REVERT: A  968 GLU cc_start: 0.7281 (mp0) cc_final: 0.6443 (mt-10)
REVERT: A 1030 ASN cc_start: 0.8314 (m-40) cc_final: 0.7843 (m-40)
REVERT: A 1057 LYS cc_start: 0.6838 (mttt) cc_final: 0.5780 (mptt)
REVERT: A 1152 GLN cc_start: 0.7891 (mt0) cc_final: 0.6694 (mp-120)
REVERT: A 1215 ASP cc_start: 0.7082 (OUTLIER) cc_final: 0.6833 (m-30)
REVERT: A 1243 GLN cc_start: 0.6678 (mm-40) cc_final: 0.6415 (mt0)
  outliers start: 17
  outliers final: 6
  residues processed: 129
  average time/residue: 0.6689
  time to fit residues: 91.4550
Evaluate side-chains
  134 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 122
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  314 THR
Chi-restraints excluded: chain A residue  402 GLU
Chi-restraints excluded: chain A residue  814 LEU
Chi-restraints excluded: chain A residue  872 MET
Chi-restraints excluded: chain A residue  895 GLU
Chi-restraints excluded: chain A residue  918 GLN
Chi-restraints excluded: chain A residue 1203 ASP
Chi-restraints excluded: chain A residue 1215 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 38 optimal weight:    5.9990
   chunk 15 optimal weight:    0.8980
   chunk 97 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 65 optimal weight:    6.9990
   chunk 43 optimal weight:    6.9990
   chunk 49 optimal weight:    0.9990
   chunk 47 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 55 optimal weight:    7.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 452 GLN
** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.179086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.126935 restraints weight = 8654.314|
|-----------------------------------------------------------------------------|
r_work (start): 0.3405 rms_B_bonded: 1.68
r_work: 0.3257 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3114 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.2335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   9518  Z= 0.160
  Angle     :  0.534   8.353  12913  Z= 0.279
  Chirality :  0.041   0.196   1490
  Planarity :  0.003   0.031   1606
  Dihedral  : 10.034  83.682   1685
  Min Nonbonded Distance : 1.923

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.22 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 16.79 %
    Favored  : 81.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.60 (0.24), residues: 1172
  helix:  1.65 (0.18), residues: 804
  sheet:  0.50 (0.64), residues: 70
  loop : -0.30 (0.34), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 954 
 TYR   0.013   0.001   TYR A 946 
 PHE   0.030   0.002   PHE A 332 
 TRP   0.010   0.001   TRP A 228 
 HIS   0.003   0.001   HIS A1151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 9518)
  covalent geometry    : angle       0.53379 (12913)
  hydrogen bonds       : bond        0.05138 (  631)
  hydrogen bonds       : angle       4.00470 ( 1851)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3791.68 seconds
wall clock time: 65 minutes 10.01 seconds (3910.01 seconds total)