Starting phenix.real_space_refine
on Fri Feb 14 03:09:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5w81_8782/02_2025/5w81_8782.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5w81_8782/02_2025/5w81_8782.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.37
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/5w81_8782/02_2025/5w81_8782.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5w81_8782/02_2025/5w81_8782.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5w81_8782/02_2025/5w81_8782.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5w81_8782/02_2025/5w81_8782.cif"
  }
  resolution = 3.37
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.008 sd=   0.209
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      55      5.16       5
     C    6091      2.51       5
     N    1571      2.21       5
     O    1668      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9393
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9329
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1173, 9329
          Classifications: {'peptide': 1173}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 41, 'TRANS': 1131}
          Chain breaks: 4
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 44
          Unresolved non-hydrogen angles: 56
          Unresolved non-hydrogen dihedrals: 36
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 28
    Chain: "A"
      Number of atoms: 64
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 64
          Unusual residues: {' MG': 2, 'ATP': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 6.04, per 1000 atoms: 0.64
  Number of scatterers: 9393
  At special positions: 0
  Unit cell: (102.5, 119.72, 113.98, 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      55     16.00
     P       6     15.00
     Mg      2     11.99
     O    1668      8.00
     N    1571      7.00
     C    6091      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.37
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2212

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 5 sheets defined
      68.2% alpha, 8.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.08
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 17
    Processing helix  chain 'A' and resid 20 through 30
    Processing helix  chain 'A' and resid 45 through 63
      removed outlier: 3.730A  pdb=" N   LEU A  49 " --> pdb=" O   ALA A  45 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   LYS A  55 " --> pdb=" O   GLU A  51 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   GLU A  56 " --> pdb=" O   ARG A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 98
      removed outlier: 3.853A  pdb=" N   ALA A  73 " --> pdb=" O   SER A  69 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   ARG A  76 " --> pdb=" O   ARG A  72 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   CYS A  77 " --> pdb=" O   ALA A  73 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   LYS A  80 " --> pdb=" O   ARG A  76 " (cutoff:3.500A)
      Proline residue:  A  81  - end of helix
      removed outlier: 3.773A  pdb=" N   LEU A  88 " --> pdb=" O   LEU A  84 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   THR A  95 " --> pdb=" O   ILE A  91 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   LYS A  96 " --> pdb=" O   GLY A  92 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   THR A  97 " --> pdb=" O   GLU A  93 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   VAL A  98 " --> pdb=" O   ALA A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 98 through 109
      removed outlier: 3.688A  pdb=" N   LEU A 102 " --> pdb=" O   VAL A  98 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   ILE A 106 " --> pdb=" O   LEU A 102 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ILE A 107 " --> pdb=" O   LEU A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 166
      removed outlier: 3.561A  pdb=" N   ARG A 135 " --> pdb=" O   LEU A 131 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   PHE A 136 " --> pdb=" O   PHE A 132 " (cutoff:3.500A)
      Proline residue:  A 141  - end of helix
      removed outlier: 3.617A  pdb=" N   ALA A 156 " --> pdb=" O   GLN A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 174
      removed outlier: 3.702A  pdb=" N   ASP A 174 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 195
      removed outlier: 3.784A  pdb=" N   LEU A 181 " --> pdb=" O   SER A 177 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   MET A 185 " --> pdb=" O   LEU A 181 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ASN A 188 " --> pdb=" O   LEU A 184 " (cutoff:3.500A)
      removed outlier: 5.322A  pdb=" N   GLY A 190 " --> pdb=" O   SER A 186 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   LYS A 191 " --> pdb=" O   ALA A 187 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   ASP A 193 " --> pdb=" O   LEU A 189 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   GLN A 194 " --> pdb=" O   GLY A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 195 through 200
      removed outlier: 3.590A  pdb=" N   ALA A 199 " --> pdb=" O   SER A 195 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 217
      removed outlier: 4.108A  pdb=" N   ILE A 204 " --> pdb=" O   HIS A 200 " (cutoff:3.500A)
      Proline residue:  A 206  - end of helix
      removed outlier: 3.522A  pdb=" N   LEU A 211 " --> pdb=" O   LEU A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 269
      removed outlier: 4.012A  pdb=" N   PHE A 225 " --> pdb=" O   ASP A 221 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ALA A 229 " --> pdb=" O   PHE A 225 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ALA A 230 " --> pdb=" O   CYS A 226 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   ILE A 231 " --> pdb=" O   ALA A 227 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   GLY A 246 " --> pdb=" O   SER A 242 " (cutoff:3.500A)
      Proline residue:  A 247  - end of helix
      removed outlier: 3.798A  pdb=" N   LEU A 254 " --> pdb=" O   ALA A 250 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   ARG A 259 " --> pdb=" O   LEU A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 277
      removed outlier: 3.792A  pdb=" N   LYS A 274 " --> pdb=" O   LEU A 270 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ALA A 275 " --> pdb=" O   HIS A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 329
      removed outlier: 4.058A  pdb=" N   ILE A 289 " --> pdb=" O   LEU A 285 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   LYS A 295 " --> pdb=" O   GLN A 291 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   LEU A 296 " --> pdb=" O   ASP A 292 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   LYS A 299 " --> pdb=" O   LYS A 295 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   PHE A 306 " --> pdb=" O   SER A 302 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   SER A 308 " --> pdb=" O   ARG A 304 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   TYR A 311 " --> pdb=" O   TYR A 307 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   ALA A 315 " --> pdb=" O   TYR A 311 " (cutoff:3.500A)
      removed outlier: 5.407A  pdb=" N   ILE A 316 " --> pdb=" O   PHE A 312 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   PHE A 317 " --> pdb=" O   PHE A 313 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ALA A 321 " --> pdb=" O   PHE A 317 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ALA A 322 " --> pdb=" O   VAL A 318 " (cutoff:3.500A)
      Proline residue:  A 325  - end of helix
      removed outlier: 3.862A  pdb=" N   LEU A 328 " --> pdb=" O   VAL A 324 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   SER A 329 " --> pdb=" O   PRO A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 353
      removed outlier: 3.719A  pdb=" N   THR A 339 " --> pdb=" O   ARG A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 353 through 377
      removed outlier: 3.805A  pdb=" N   GLY A 357 " --> pdb=" O   ARG A 353 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   MET A 361 " --> pdb=" O   GLY A 357 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   ARG A 367 " --> pdb=" O   TYR A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 472
      removed outlier: 3.678A  pdb=" N   LEU A 467 " --> pdb=" O   LYS A 463 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 500 through 507
    Processing helix  chain 'A' and resid 513 through 523
      removed outlier: 3.996A  pdb=" N   LYS A 517 " --> pdb=" O   GLU A 513 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 525 through 531
      removed outlier: 3.571A  pdb=" N   LEU A 529 " --> pdb=" O   LEU A 525 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 548 through 563
      removed outlier: 3.691A  pdb=" N   LYS A 552 " --> pdb=" O   SER A 548 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   ALA A 553 " --> pdb=" O   GLY A 549 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ALA A 560 " --> pdb=" O   ALA A 556 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   ARG A 563 " --> pdb=" O   ARG A 559 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 589
    Processing helix  chain 'A' and resid 605 through 612
    Processing helix  chain 'A' and resid 628 through 635
    Processing helix  chain 'A' and resid 845 through 854
      removed outlier: 4.091A  pdb=" N   ASN A 854 " --> pdb=" O   TYR A 850 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 854 through 886
      removed outlier: 4.044A  pdb=" N   LEU A 858 " --> pdb=" O   ASN A 854 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   PHE A 863 " --> pdb=" O   TYR A 859 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   LEU A 865 " --> pdb=" O   LEU A 861 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   SER A 875 " --> pdb=" O   GLU A 871 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   PHE A 880 " --> pdb=" O   VAL A 876 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   ILE A 882 " --> pdb=" O   GLY A 878 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   GLU A 885 " --> pdb=" O   LEU A 881 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 921 through 935
      removed outlier: 3.533A  pdb=" N   ILE A 926 " --> pdb=" O   TYR A 922 " (cutoff:3.500A)
      removed outlier: 5.083A  pdb=" N   GLU A 932 " --> pdb=" O   VAL A 928 " (cutoff:3.500A)
      removed outlier: 6.012A  pdb=" N   SER A 933 " --> pdb=" O   ALA A 929 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 938 through 966
      removed outlier: 3.560A  pdb=" N   LEU A 943 " --> pdb=" O   PHE A 939 " (cutoff:3.500A)
      Proline residue:  A 944  - end of helix
      removed outlier: 4.109A  pdb=" N   SER A 953 " --> pdb=" O   THR A 949 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   MET A 960 " --> pdb=" O   LEU A 956 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   HIS A 962 " --> pdb=" O   GLN A 958 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 968 through 975
      removed outlier: 3.600A  pdb=" N   MET A 975 " --> pdb=" O   VAL A 971 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 976 through 994
      removed outlier: 3.517A  pdb=" N   ILE A 980 " --> pdb=" O   LYS A 976 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   ARG A 983 " --> pdb=" O   ARG A 979 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   PHE A 984 " --> pdb=" O   ILE A 980 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ASP A 987 " --> pdb=" O   ARG A 983 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   MET A 988 " --> pdb=" O   PHE A 984 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   ALA A 989 " --> pdb=" O   THR A 985 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 994 through 1019
      removed outlier: 3.745A  pdb=" N   VAL A1003 " --> pdb=" O   MET A 999 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   VAL A1019 " --> pdb=" O   VAL A1015 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1022 through 1056
      removed outlier: 3.930A  pdb=" N   ALA A1026 " --> pdb=" O   TYR A1022 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   ALA A1027 " --> pdb=" O   ILE A1023 " (cutoff:3.500A)
      Proline residue:  A1029  - end of helix
      removed outlier: 3.852A  pdb=" N   ILE A1032 " --> pdb=" O   THR A1028 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   THR A1044 " --> pdb=" O   TYR A1040 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   GLN A1046 " --> pdb=" O   LEU A1042 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   GLN A1047 " --> pdb=" O   ARG A1043 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLN A1050 " --> pdb=" O   GLN A1046 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   LEU A1051 " --> pdb=" O   GLN A1047 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1056 through 1069
      removed outlier: 4.136A  pdb=" N   PHE A1060 " --> pdb=" O   ARG A1056 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   LYS A1068 " --> pdb=" O   ILE A1064 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   GLY A1069 " --> pdb=" O   MET A1065 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1069 through 1076
      removed outlier: 3.615A  pdb=" N   ILE A1073 " --> pdb=" O   GLY A1069 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1078 through 1126
      removed outlier: 3.744A  pdb=" N   HIS A1093 " --> pdb=" O   THR A1089 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   THR A1096 " --> pdb=" O   THR A1092 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ASP A1112 " --> pdb=" O   LEU A1108 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   PHE A1117 " --> pdb=" O   ILE A1113 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   PHE A1118 " --> pdb=" O   LEU A1114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1137 through 1148
    Processing helix  chain 'A' and resid 1150 through 1166
      removed outlier: 3.617A  pdb=" N   ALA A1160 " --> pdb=" O   ALA A1156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1166 through 1176
      removed outlier: 3.875A  pdb=" N   ARG A1170 " --> pdb=" O   ARG A1166 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   VAL A1171 " --> pdb=" O   SER A1167 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   PHE A1174 " --> pdb=" O   ARG A1170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1250 through 1259
      removed outlier: 3.892A  pdb=" N   PHE A1255 " --> pdb=" O   LYS A1251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1279 through 1286
      removed outlier: 3.578A  pdb=" N   ALA A1286 " --> pdb=" O   LYS A1282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1300 through 1306
    Processing helix  chain 'A' and resid 1312 through 1323
    Processing helix  chain 'A' and resid 1325 through 1331
      removed outlier: 3.870A  pdb=" N   ILE A1329 " --> pdb=" O   LEU A1325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1348 through 1364
      removed outlier: 3.770A  pdb=" N   SER A1360 " --> pdb=" O   CYS A1356 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LEU A1362 " --> pdb=" O   ALA A1358 " (cutoff:3.500A)
      removed outlier: 4.225A  pdb=" N   GLY A1364 " --> pdb=" O   SER A1360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1378 through 1393
      removed outlier: 3.707A  pdb=" N   LYS A1383 " --> pdb=" O   PRO A1379 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   VAL A1384 " --> pdb=" O   VAL A1380 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   THR A1388 " --> pdb=" O   VAL A1384 " (cutoff:3.500A)
      removed outlier: 4.916A  pdb=" N   GLN A1391 " --> pdb=" O   LYS A1387 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   SER A1392 " --> pdb=" O   THR A1388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1407 through 1411
      removed outlier: 4.016A  pdb=" N   GLU A1410 " --> pdb=" O   PRO A1407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1427 through 1435
    Processing helix  chain 'A' and resid 1446 through 1451
      removed outlier: 3.907A  pdb=" N   LEU A1450 " --> pdb=" O   GLU A1446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1452 through 1457
    Processing sheet with id=AA1, first strand: chain 'A' and resid 440 through 446
      removed outlier: 4.947A  pdb=" N   VAL A 398 " --> pdb=" O   ASP A 442 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   SER A 444 " --> pdb=" O   GLN A 396 " (cutoff:3.500A)
      removed outlier: 7.011A  pdb=" N   GLN A 396 " --> pdb=" O   SER A 444 " (cutoff:3.500A)
      removed outlier: 7.644A  pdb=" N   LYS A 446 " --> pdb=" O   GLU A 394 " (cutoff:3.500A)
      removed outlier: 7.905A  pdb=" N   GLU A 394 " --> pdb=" O   LYS A 446 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   LYS A 480 " --> pdb=" O   GLN A 396 " (cutoff:3.500A)
      removed outlier: 4.727A  pdb=" N   VAL A 398 " --> pdb=" O   SER A 478 " (cutoff:3.500A)
      removed outlier: 7.284A  pdb=" N   SER A 478 " --> pdb=" O   VAL A 398 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 487 through 490
      removed outlier: 6.667A  pdb=" N   TYR A 568 " --> pdb=" O   ILE A 600 " (cutoff:3.500A)
      removed outlier: 8.045A  pdb=" N   VAL A 602 " --> pdb=" O   TYR A 568 " (cutoff:3.500A)
      removed outlier: 7.572A  pdb=" N   LEU A 570 " --> pdb=" O   VAL A 602 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   LYS A 614 " --> pdb=" O   MET A 452 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   ILE A 615 " --> pdb=" O   TYR A 626 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   TYR A 626 " --> pdb=" O   ILE A 615 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   LEU A 617 " --> pdb=" O   PHE A 624 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1228 through 1235
      removed outlier: 6.755A  pdb=" N   LYS A1229 " --> pdb=" O   THR A1217 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   THR A1217 " --> pdb=" O   LYS A1229 " (cutoff:3.500A)
      removed outlier: 5.171A  pdb=" N   LEU A1231 " --> pdb=" O   ASN A1215 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1228 through 1235
      removed outlier: 6.755A  pdb=" N   LYS A1229 " --> pdb=" O   THR A1217 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   THR A1217 " --> pdb=" O   LYS A1229 " (cutoff:3.500A)
      removed outlier: 5.171A  pdb=" N   LEU A1231 " --> pdb=" O   ASN A1215 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1287 through 1290
      removed outlier: 6.203A  pdb=" N   GLY A1288 " --> pdb=" O   LEU A1369 " (cutoff:3.500A)
      removed outlier: 7.549A  pdb=" N   ASP A1371 " --> pdb=" O   GLY A1288 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   VAL A1290 " --> pdb=" O   ASP A1371 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   LEU A1368 " --> pdb=" O   LEU A1399 " (cutoff:3.500A)
      removed outlier: 8.039A  pdb=" N   SER A1401 " --> pdb=" O   LEU A1368 " (cutoff:3.500A)
      removed outlier: 7.292A  pdb=" N   LEU A1370 " --> pdb=" O   SER A1401 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   ARG A1240 " --> pdb=" O   SER A1413 " (cutoff:3.500A)
      removed outlier: 8.162A  pdb=" N   LEU A1415 " --> pdb=" O   ARG A1240 " (cutoff:3.500A)
      removed outlier: 6.126A  pdb=" N   GLY A1242 " --> pdb=" O   LEU A1415 " (cutoff:3.500A)
      removed outlier: 7.460A  pdb=" N   MET A1417 " --> pdb=" O   GLY A1242 " (cutoff:3.500A)
      removed outlier: 6.969A  pdb=" N   LEU A1244 " --> pdb=" O   MET A1417 " (cutoff:3.500A)

    507 hydrogen bonds defined for protein.
    1497 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: 3.88

  Time building geometry restraints manager: 2.78 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1507
        1.33 -     1.45: 2524
        1.45 -     1.57: 5462
        1.57 -     1.69: 10
        1.69 -     1.81: 94
  Bond restraints: 9597
  Sorted by residual:
  bond pdb=" C4  ATP A1501 "
       pdb=" C5  ATP A1501 "
    ideal  model  delta    sigma   weight residual
    1.388  1.473 -0.085 1.00e-02 1.00e+04 7.21e+01
  bond pdb=" C4  ATP A1502 "
       pdb=" C5  ATP A1502 "
    ideal  model  delta    sigma   weight residual
    1.388  1.471 -0.083 1.00e-02 1.00e+04 6.84e+01
  bond pdb=" C5  ATP A1501 "
       pdb=" C6  ATP A1501 "
    ideal  model  delta    sigma   weight residual
    1.409  1.486 -0.077 1.00e-02 1.00e+04 5.91e+01
  bond pdb=" C5  ATP A1502 "
       pdb=" C6  ATP A1502 "
    ideal  model  delta    sigma   weight residual
    1.409  1.478 -0.069 1.00e-02 1.00e+04 4.72e+01
  bond pdb=" C5  ATP A1502 "
       pdb=" N7  ATP A1502 "
    ideal  model  delta    sigma   weight residual
    1.387  1.337  0.050 1.00e-02 1.00e+04 2.48e+01
  ... (remaining 9592 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.06: 12902
        4.06 -     8.11: 73
        8.11 -    12.17: 6
       12.17 -    16.22: 0
       16.22 -    20.28: 4
  Bond angle restraints: 12985
  Sorted by residual:
  angle pdb=" PB  ATP A1501 "
        pdb=" O3B ATP A1501 "
        pdb=" PG  ATP A1501 "
      ideal   model   delta    sigma   weight residual
     139.87  119.59   20.28 1.00e+00 1.00e+00 4.11e+02
  angle pdb=" PB  ATP A1502 "
        pdb=" O3B ATP A1502 "
        pdb=" PG  ATP A1502 "
      ideal   model   delta    sigma   weight residual
     139.87  121.37   18.50 1.00e+00 1.00e+00 3.42e+02
  angle pdb=" PA  ATP A1501 "
        pdb=" O3A ATP A1501 "
        pdb=" PB  ATP A1501 "
      ideal   model   delta    sigma   weight residual
     136.83  119.66   17.17 1.00e+00 1.00e+00 2.95e+02
  angle pdb=" PA  ATP A1502 "
        pdb=" O3A ATP A1502 "
        pdb=" PB  ATP A1502 "
      ideal   model   delta    sigma   weight residual
     136.83  120.27   16.56 1.00e+00 1.00e+00 2.74e+02
  angle pdb=" C5  ATP A1501 "
        pdb=" C4  ATP A1501 "
        pdb=" N3  ATP A1501 "
      ideal   model   delta    sigma   weight residual
     126.80  118.54    8.26 1.00e+00 1.00e+00 6.82e+01
  ... (remaining 12980 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.38: 5258
       17.38 -    34.75: 379
       34.75 -    52.13: 117
       52.13 -    69.51: 24
       69.51 -    86.88: 3
  Dihedral angle restraints: 5781
    sinusoidal: 2362
      harmonic: 3419
  Sorted by residual:
  dihedral pdb=" CA  TRP A1205 "
           pdb=" C   TRP A1205 "
           pdb=" N   PRO A1206 "
           pdb=" CA  PRO A1206 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.37  -27.63     0      5.00e+00 4.00e-02 3.05e+01
  dihedral pdb=" C   ILE A 332 "
           pdb=" N   ILE A 332 "
           pdb=" CA  ILE A 332 "
           pdb=" CB  ILE A 332 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -132.57   10.57     0      2.50e+00 1.60e-01 1.79e+01
  dihedral pdb=" CA  GLU A 218 "
           pdb=" C   GLU A 218 "
           pdb=" N   LEU A 219 "
           pdb=" CA  LEU A 219 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.64   19.36     0      5.00e+00 4.00e-02 1.50e+01
  ... (remaining 5778 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 1002
       0.053 -    0.106: 347
       0.106 -    0.159: 98
       0.159 -    0.212: 34
       0.212 -    0.265: 9
  Chirality restraints: 1490
  Sorted by residual:
  chirality pdb=" CA  GLU A1406 "
            pdb=" N   GLU A1406 "
            pdb=" C   GLU A1406 "
            pdb=" CB  GLU A1406 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.75e+00
  chirality pdb=" CA  GLU A 115 "
            pdb=" N   GLU A 115 "
            pdb=" C   GLU A 115 "
            pdb=" CB  GLU A 115 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.70e+00
  chirality pdb=" CA  LYS A1335 "
            pdb=" N   LYS A1335 "
            pdb=" C   LYS A1335 "
            pdb=" CB  LYS A1335 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.41e+00
  ... (remaining 1487 not shown)

  Planarity restraints: 1589
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 324 "   -0.029 5.00e-02 4.00e+02   4.45e-02 3.17e+00
        pdb=" N   PRO A 325 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO A 325 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 325 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A1448 "   -0.008 2.00e-02 2.50e+03   1.66e-02 2.74e+00
        pdb=" C   LEU A1448 "    0.029 2.00e-02 2.50e+03
        pdb=" O   LEU A1448 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   LYS A1449 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A1057 "   -0.025 5.00e-02 4.00e+02   3.76e-02 2.27e+00
        pdb=" N   PRO A1058 "    0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO A1058 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A1058 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1586 not shown)

  Histogram of nonbonded interaction distances:
        1.94 -     2.53: 13
        2.53 -     3.12: 6394
        3.12 -     3.72: 13963
        3.72 -     4.31: 19019
        4.31 -     4.90: 31491
  Nonbonded interactions: 70880
  Sorted by model distance:
  nonbonded pdb=" O2B ATP A1502 "
            pdb="MG    MG A1504 "
     model   vdw
     1.940 2.170
  nonbonded pdb=" O2B ATP A1501 "
            pdb="MG    MG A1503 "
     model   vdw
     1.994 2.170
  nonbonded pdb=" OE1 GLN A1292 "
            pdb="MG    MG A1504 "
     model   vdw
     2.016 2.170
  nonbonded pdb=" OG  SER A 464 "
            pdb="MG    MG A1503 "
     model   vdw
     2.148 2.170
  nonbonded pdb=" O   ARG A1453 "
            pdb=" OG  SER A1457 "
     model   vdw
     2.155 3.040
  ... (remaining 70875 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=0.65 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.710
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     26.350
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5897
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      :  0.008   0.085   9597  Z= 0.530
  Angle     :  1.261  20.279  12985  Z= 0.900
  Chirality :  0.064   0.265   1490
  Planarity :  0.004   0.044   1589
  Dihedral  : 13.886  86.881   3569
  Min Nonbonded Distance : 1.940

Molprobity Statistics.
  All-atom Clashscore : 1.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.11 (0.20), residues: 1163
  helix: -1.81 (0.15), residues: 693
  sheet: -2.73 (0.53), residues: 74
  loop : -2.05 (0.29), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 402 
 HIS   0.005   0.001   HIS A1087 
 PHE   0.017   0.002   PHE A 136 
 TYR   0.015   0.002   TYR A 922 
 ARG   0.005   0.001   ARG A 554 

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

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

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 297
  time to evaluate  : 1.091 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 ASP cc_start: 0.7173 (t0) cc_final: 0.6927 (t0)
REVERT: A   60 GLU cc_start: 0.6832 (tm-30) cc_final: 0.5829 (tm-30)
REVERT: A   70 LEU cc_start: 0.7632 (tp) cc_final: 0.7405 (tt)
REVERT: A   77 CYS cc_start: 0.6213 (p) cc_final: 0.5951 (p)
REVERT: A  100 PRO cc_start: 0.9136 (Cg_exo) cc_final: 0.8888 (Cg_endo)
REVERT: A  204 ILE cc_start: 0.4869 (mm) cc_final: 0.4560 (mt)
REVERT: A  326 HIS cc_start: 0.8549 (t70) cc_final: 0.8325 (t-90)
REVERT: A  384 MET cc_start: 0.6948 (mmp) cc_final: 0.6201 (mmm)
REVERT: A  458 SER cc_start: 0.8544 (m) cc_final: 0.7877 (t)
REVERT: A  461 SER cc_start: 0.8350 (m) cc_final: 0.7562 (t)
REVERT: A  497 MET cc_start: 0.5461 (mtp) cc_final: 0.5168 (ttm)
REVERT: A  513 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8321 (tp30)
REVERT: A  527 GLU cc_start: 0.7911 (tt0) cc_final: 0.7553 (mp0)
REVERT: A  578 ASP cc_start: 0.7289 (m-30) cc_final: 0.6669 (m-30)
REVERT: A  625 PHE cc_start: 0.7618 (t80) cc_final: 0.7313 (t80)
REVERT: A  854 ASN cc_start: 0.7330 (t0) cc_final: 0.6396 (t0)
REVERT: A 1008 VAL cc_start: 0.6781 (t) cc_final: 0.6437 (t)
REVERT: A 1231 LEU cc_start: 0.8450 (tt) cc_final: 0.8189 (mm)
REVERT: A 1278 MET cc_start: 0.7323 (tpp) cc_final: 0.7099 (tpp)
REVERT: A 1285 LYS cc_start: 0.8524 (mmmm) cc_final: 0.8262 (mttt)
REVERT: A 1322 GLU cc_start: 0.8346 (tt0) cc_final: 0.7953 (tt0)
REVERT: A 1336 LEU cc_start: 0.7841 (mp) cc_final: 0.7244 (tt)
REVERT: A 1342 TYR cc_start: 0.4866 (t80) cc_final: 0.4593 (t80)
REVERT: A 1374 SER cc_start: 0.8541 (m) cc_final: 0.8262 (p)
REVERT: A 1416 MET cc_start: 0.7109 (ttp) cc_final: 0.6838 (tmm)
REVERT: A 1428 ILE cc_start: 0.8161 (mm) cc_final: 0.7408 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 297
  average time/residue: 0.2494
  time to fit residues: 100.6995
Evaluate side-chains
  177 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 1.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 98 optimal weight:    0.4980
   chunk 88 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 91 optimal weight:    0.3980
   chunk 35 optimal weight:    1.9990
   chunk 55 optimal weight:    0.6980
   chunk 68 optimal weight:    0.7980
   chunk 106 optimal weight:    0.9980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 148 HIS
A 288 ASN
** A 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1062 HIS
A1210 GLN
A1372 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.144032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.121504 restraints weight = 17459.590|
|-----------------------------------------------------------------------------|
r_work (start): 0.3553 rms_B_bonded: 3.22
r_work: 0.3429 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3428
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3428 r_free = 0.3428    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.65   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3428 r_free = 0.3428    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3428
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7214
moved from start:          0.4184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9597  Z= 0.212
  Angle     :  0.660   8.442  12985  Z= 0.335
  Chirality :  0.043   0.256   1490
  Planarity :  0.005   0.066   1589
  Dihedral  :  8.289  89.912   1335
  Min Nonbonded Distance : 1.935

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 12.85 %
    Favored  : 83.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.80 (0.23), residues: 1163
  helix:  0.26 (0.18), residues: 737
  sheet: -2.19 (0.51), residues: 81
  loop : -1.65 (0.31), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A1275 
 HIS   0.008   0.001   HIS A 608 
 PHE   0.019   0.002   PHE A1115 
 TYR   0.023   0.002   TYR A 921 
 ARG   0.008   0.001   ARG A 335 

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

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

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 204
  time to evaluate  : 0.973 
Fit side-chains
   revert: symmetry clash
REVERT: A    7 GLU cc_start: 0.7003 (tp30) cc_final: 0.6392 (mp0)
REVERT: A   26 LYS cc_start: 0.7698 (ttmm) cc_final: 0.7268 (ttpp)
REVERT: A   36 ASP cc_start: 0.7261 (t0) cc_final: 0.7045 (t0)
REVERT: A  317 PHE cc_start: 0.6530 (t80) cc_final: 0.6042 (t80)
REVERT: A  513 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8546 (tp30)
REVERT: A  527 GLU cc_start: 0.8118 (tt0) cc_final: 0.7849 (mp0)
REVERT: A  619 HIS cc_start: 0.7830 (t-170) cc_final: 0.7494 (t-90)
REVERT: A  854 ASN cc_start: 0.7726 (t0) cc_final: 0.7353 (t0)
REVERT: A  977 THR cc_start: 0.8514 (t) cc_final: 0.8075 (m)
REVERT: A  987 ASP cc_start: 0.7343 (m-30) cc_final: 0.7105 (m-30)
REVERT: A 1249 SER cc_start: 0.9311 (t) cc_final: 0.9030 (t)
REVERT: A 1303 MET cc_start: 0.8284 (mtp) cc_final: 0.8059 (mtp)
REVERT: A 1383 LYS cc_start: 0.8541 (ttpp) cc_final: 0.8201 (tptt)
REVERT: A 1416 MET cc_start: 0.7327 (ttp) cc_final: 0.6985 (tmm)
REVERT: A 1437 HIS cc_start: 0.7743 (m-70) cc_final: 0.7177 (m-70)
REVERT: A 1458 MET cc_start: 0.4788 (tpp) cc_final: 0.4481 (tpp)
  outliers start: 32
  outliers final: 16
  residues processed: 225
  average time/residue: 0.1899
  time to fit residues: 62.4895
Evaluate side-chains
  172 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 156
  time to evaluate  : 1.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  224 SER
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain A residue  991 ILE
Chi-restraints excluded: chain A residue 1121 LEU
Chi-restraints excluded: chain A residue 1220 TYR
Chi-restraints excluded: chain A residue 1262 VAL
Chi-restraints excluded: chain A residue 1361 ILE
Chi-restraints excluded: chain A residue 1369 LEU
Chi-restraints excluded: chain A residue 1380 VAL
Chi-restraints excluded: chain A residue 1423 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 89 optimal weight:    0.3980
   chunk 35 optimal weight:    1.9990
   chunk 42 optimal weight:    6.9990
   chunk 97 optimal weight:    2.9990
   chunk 114 optimal weight:    3.9990
   chunk 78 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 3 optimal weight:    0.2980
   chunk 70 optimal weight:    0.2980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 223 ASN
A 271 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.142737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.119938 restraints weight = 17888.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.3556 rms_B_bonded: 3.33
r_work: 0.3431 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3444
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3444 r_free = 0.3444    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3443 r_free = 0.3443    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3443
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7495
moved from start:          0.5836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9597  Z= 0.185
  Angle     :  0.625   9.599  12985  Z= 0.313
  Chirality :  0.040   0.202   1490
  Planarity :  0.004   0.067   1589
  Dihedral  :  7.593  88.151   1335
  Min Nonbonded Distance : 1.933

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 16.40 %
    Favored  : 80.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.06 (0.24), residues: 1163
  helix:  0.84 (0.18), residues: 739
  sheet: -1.66 (0.57), residues: 76
  loop : -1.45 (0.31), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 217 
 HIS   0.004   0.001   HIS A 148 
 PHE   0.017   0.001   PHE A 136 
 TYR   0.021   0.002   TYR A 850 
 ARG   0.006   0.001   ARG A1447 

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

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

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 192
  time to evaluate  : 1.085 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    7 GLU cc_start: 0.7341 (tp30) cc_final: 0.6727 (mp0)
REVERT: A   51 GLU cc_start: 0.8825 (pp20) cc_final: 0.8534 (pp20)
REVERT: A  123 PHE cc_start: 0.5529 (t80) cc_final: 0.5127 (m-80)
REVERT: A  317 PHE cc_start: 0.6555 (t80) cc_final: 0.6213 (t80)
REVERT: A  497 MET cc_start: 0.6689 (ttm) cc_final: 0.6296 (mtp)
REVERT: A  619 HIS cc_start: 0.8133 (t-170) cc_final: 0.7875 (t-90)
REVERT: A  977 THR cc_start: 0.8594 (t) cc_final: 0.8141 (m)
REVERT: A 1383 LYS cc_start: 0.8548 (ttpp) cc_final: 0.8238 (tptt)
REVERT: A 1400 LEU cc_start: 0.8859 (mm) cc_final: 0.8466 (mp)
REVERT: A 1437 HIS cc_start: 0.7930 (m-70) cc_final: 0.7439 (m-70)
  outliers start: 30
  outliers final: 16
  residues processed: 212
  average time/residue: 0.2116
  time to fit residues: 64.9143
Evaluate side-chains
  179 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 163
  time to evaluate  : 1.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  224 SER
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  312 PHE
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain A residue  481 ILE
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  990 THR
Chi-restraints excluded: chain A residue 1092 THR
Chi-restraints excluded: chain A residue 1121 LEU
Chi-restraints excluded: chain A residue 1262 VAL
Chi-restraints excluded: chain A residue 1327 THR
Chi-restraints excluded: chain A residue 1369 LEU
Chi-restraints excluded: chain A residue 1380 VAL
Chi-restraints excluded: chain A residue 1423 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 0 optimal weight:    8.9990
   chunk 106 optimal weight:    0.9990
   chunk 109 optimal weight:    0.9980
   chunk 74 optimal weight:    4.9990
   chunk 87 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9980
   chunk 57 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 2 optimal weight:    0.8980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A1004 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.138871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.116193 restraints weight = 18262.986|
|-----------------------------------------------------------------------------|
r_work (start): 0.3531 rms_B_bonded: 3.29
r_work: 0.3404 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3406
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3406 r_free = 0.3406    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3406 r_free = 0.3406    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3406
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.7443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9597  Z= 0.216
  Angle     :  0.625   9.195  12985  Z= 0.312
  Chirality :  0.040   0.197   1490
  Planarity :  0.004   0.069   1589
  Dihedral  :  7.567  86.573   1335
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 17.69 %
    Favored  : 78.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.24), residues: 1163
  helix:  0.95 (0.19), residues: 744
  sheet: -1.55 (0.57), residues: 75
  loop : -1.43 (0.31), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  57 
 HIS   0.005   0.001   HIS A 200 
 PHE   0.017   0.001   PHE A 136 
 TYR   0.017   0.002   TYR A1342 
 ARG   0.004   0.001   ARG A1318 

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

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

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 195
  time to evaluate  : 1.095 
Fit side-chains
REVERT: A   48 ILE cc_start: 0.7982 (OUTLIER) cc_final: 0.7768 (mm)
REVERT: A   51 GLU cc_start: 0.8970 (pp20) cc_final: 0.8688 (pp20)
REVERT: A  123 PHE cc_start: 0.5767 (t80) cc_final: 0.5132 (m-80)
REVERT: A  191 LYS cc_start: 0.8518 (ttpp) cc_final: 0.8223 (ttpp)
REVERT: A  491 SER cc_start: 0.9400 (OUTLIER) cc_final: 0.8893 (p)
REVERT: A  977 THR cc_start: 0.8795 (t) cc_final: 0.8486 (m)
REVERT: A  979 ARG cc_start: 0.8001 (ttt90) cc_final: 0.7797 (mtp85)
REVERT: A  999 MET cc_start: 0.8157 (tpt) cc_final: 0.7913 (mmm)
REVERT: A 1322 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8466 (mt-10)
REVERT: A 1416 MET cc_start: 0.8603 (tmm) cc_final: 0.8020 (tmm)
REVERT: A 1437 HIS cc_start: 0.8029 (m-70) cc_final: 0.7571 (m-70)
  outliers start: 38
  outliers final: 20
  residues processed: 226
  average time/residue: 0.2174
  time to fit residues: 70.0512
Evaluate side-chains
  183 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 161
  time to evaluate  : 1.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  224 SER
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  312 PHE
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain A residue  481 ILE
Chi-restraints excluded: chain A residue  491 SER
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  990 THR
Chi-restraints excluded: chain A residue 1028 THR
Chi-restraints excluded: chain A residue 1092 THR
Chi-restraints excluded: chain A residue 1108 LEU
Chi-restraints excluded: chain A residue 1213 VAL
Chi-restraints excluded: chain A residue 1369 LEU
Chi-restraints excluded: chain A residue 1380 VAL
Chi-restraints excluded: chain A residue 1423 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 90 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 88 optimal weight:    0.7980
   chunk 75 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   chunk 66 optimal weight:    8.9990
   chunk 11 optimal weight:    0.0570
   chunk 54 optimal weight:    0.5980
   chunk 15 optimal weight:    0.7980
   chunk 46 optimal weight:    2.9990
   overall best weight:    0.6498

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

Flipped N/Q/H residues before XYZ refinement:
A 291 GLN
A 620 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.139141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.116337 restraints weight = 18411.773|
|-----------------------------------------------------------------------------|
r_work (start): 0.3513 rms_B_bonded: 3.34
r_work: 0.3390 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3406
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3406 r_free = 0.3406    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3406 r_free = 0.3406    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.52   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3406
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.8029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9597  Z= 0.168
  Angle     :  0.589   7.738  12985  Z= 0.291
  Chirality :  0.040   0.192   1490
  Planarity :  0.004   0.070   1589
  Dihedral  :  7.108  87.325   1335
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 20.16 %
    Favored  : 76.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.24), residues: 1163
  helix:  1.15 (0.19), residues: 736
  sheet: -1.26 (0.57), residues: 75
  loop : -1.41 (0.30), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  57 
 HIS   0.003   0.001   HIS A 200 
 PHE   0.019   0.001   PHE A 136 
 TYR   0.019   0.001   TYR A1342 
 ARG   0.002   0.000   ARG A1447 

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

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

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 185
  time to evaluate  : 0.986 
Fit side-chains
REVERT: A    1 MET cc_start: 0.7555 (mmt) cc_final: 0.7159 (mmt)
REVERT: A   51 GLU cc_start: 0.8979 (pp20) cc_final: 0.8730 (pp20)
REVERT: A  123 PHE cc_start: 0.5871 (t80) cc_final: 0.5127 (m-80)
REVERT: A  191 LYS cc_start: 0.8485 (ttpp) cc_final: 0.8279 (tttp)
REVERT: A  233 LEU cc_start: 0.8609 (tp) cc_final: 0.8311 (mm)
REVERT: A  977 THR cc_start: 0.8841 (OUTLIER) cc_final: 0.8544 (m)
REVERT: A  999 MET cc_start: 0.8193 (tpt) cc_final: 0.7942 (mmm)
REVERT: A 1052 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8306 (tm-30)
REVERT: A 1265 ASP cc_start: 0.8501 (m-30) cc_final: 0.8251 (m-30)
REVERT: A 1322 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8588 (mt-10)
REVERT: A 1402 GLU cc_start: 0.7936 (tp30) cc_final: 0.7581 (tm-30)
REVERT: A 1416 MET cc_start: 0.8488 (tmm) cc_final: 0.7090 (tmm)
REVERT: A 1418 ASP cc_start: 0.7773 (t0) cc_final: 0.7463 (t0)
REVERT: A 1437 HIS cc_start: 0.8115 (m-70) cc_final: 0.7688 (m-70)
  outliers start: 31
  outliers final: 18
  residues processed: 205
  average time/residue: 0.2271
  time to fit residues: 67.9167
Evaluate side-chains
  188 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 169
  time to evaluate  : 1.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 ASN
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  224 SER
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  481 ILE
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  977 THR
Chi-restraints excluded: chain A residue  990 THR
Chi-restraints excluded: chain A residue 1028 THR
Chi-restraints excluded: chain A residue 1030 LEU
Chi-restraints excluded: chain A residue 1092 THR
Chi-restraints excluded: chain A residue 1121 LEU
Chi-restraints excluded: chain A residue 1268 ILE
Chi-restraints excluded: chain A residue 1294 VAL
Chi-restraints excluded: chain A residue 1380 VAL
Chi-restraints excluded: chain A residue 1423 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 76 optimal weight:    0.8980
   chunk 104 optimal weight:    5.9990
   chunk 72 optimal weight:    0.9990
   chunk 73 optimal weight:    0.9980
   chunk 52 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 46 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 65 optimal weight:    8.9990
   chunk 88 optimal weight:    0.9990
   overall best weight:    0.9382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.136302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.113734 restraints weight = 18422.031|
|-----------------------------------------------------------------------------|
r_work (start): 0.3496 rms_B_bonded: 3.23
r_work: 0.3372 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3373
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3373 r_free = 0.3373    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.52   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3373 r_free = 0.3373    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3373
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.8642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9597  Z= 0.203
  Angle     :  0.605   9.235  12985  Z= 0.301
  Chirality :  0.040   0.191   1490
  Planarity :  0.004   0.074   1589
  Dihedral  :  6.808  88.872   1335
  Min Nonbonded Distance : 1.906

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 21.64 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.24), residues: 1163
  helix:  1.10 (0.19), residues: 742
  sheet: -1.16 (0.57), residues: 75
  loop : -1.49 (0.30), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  57 
 HIS   0.006   0.001   HIS A 200 
 PHE   0.018   0.001   PHE A 136 
 TYR   0.020   0.001   TYR A1342 
 ARG   0.008   0.001   ARG A 304 

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

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

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 182
  time to evaluate  : 1.070 
Fit side-chains
REVERT: A   51 GLU cc_start: 0.9035 (pp20) cc_final: 0.8718 (pp20)
REVERT: A  102 LEU cc_start: 0.9275 (tp) cc_final: 0.9012 (tp)
REVERT: A  191 LYS cc_start: 0.8510 (ttpp) cc_final: 0.8196 (ttpp)
REVERT: A  282 MET cc_start: 0.8484 (tpp) cc_final: 0.8254 (mmt)
REVERT: A  304 ARG cc_start: 0.8342 (ttt-90) cc_final: 0.8003 (ttt-90)
REVERT: A  977 THR cc_start: 0.8852 (OUTLIER) cc_final: 0.8543 (m)
REVERT: A  999 MET cc_start: 0.8178 (tpt) cc_final: 0.7958 (mmm)
REVERT: A 1265 ASP cc_start: 0.8519 (m-30) cc_final: 0.8285 (m-30)
REVERT: A 1322 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8547 (mt-10)
REVERT: A 1406 GLU cc_start: 0.8093 (pt0) cc_final: 0.7482 (tm-30)
REVERT: A 1416 MET cc_start: 0.8613 (tmm) cc_final: 0.7194 (tmm)
REVERT: A 1417 MET cc_start: 0.8566 (ttm) cc_final: 0.7720 (ttt)
REVERT: A 1418 ASP cc_start: 0.7795 (t0) cc_final: 0.7476 (t0)
REVERT: A 1437 HIS cc_start: 0.8200 (m-70) cc_final: 0.7756 (m-70)
  outliers start: 34
  outliers final: 19
  residues processed: 207
  average time/residue: 0.2013
  time to fit residues: 59.4909
Evaluate side-chains
  191 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 171
  time to evaluate  : 1.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 ASN
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  224 SER
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain A residue  452 MET
Chi-restraints excluded: chain A residue  481 ILE
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  977 THR
Chi-restraints excluded: chain A residue  990 THR
Chi-restraints excluded: chain A residue 1028 THR
Chi-restraints excluded: chain A residue 1030 LEU
Chi-restraints excluded: chain A residue 1092 THR
Chi-restraints excluded: chain A residue 1114 LEU
Chi-restraints excluded: chain A residue 1217 THR
Chi-restraints excluded: chain A residue 1423 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 81 optimal weight:    0.7980
   chunk 75 optimal weight:    5.9990
   chunk 24 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9990
   chunk 13 optimal weight:    4.9990
   chunk 69 optimal weight:    1.9990
   chunk 89 optimal weight:    5.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A 853 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.133845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.111363 restraints weight = 18623.349|
|-----------------------------------------------------------------------------|
r_work (start): 0.3459 rms_B_bonded: 3.29
r_work: 0.3332 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3331
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3331 r_free = 0.3331    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3331 r_free = 0.3331    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3331
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8018
moved from start:          0.9152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9597  Z= 0.222
  Angle     :  0.619  10.968  12985  Z= 0.306
  Chirality :  0.040   0.191   1490
  Planarity :  0.004   0.079   1589
  Dihedral  :  6.671  86.734   1335
  Min Nonbonded Distance : 1.900

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.92 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 22.63 %
    Favored  : 74.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.24), residues: 1163
  helix:  1.14 (0.19), residues: 732
  sheet: -1.04 (0.58), residues: 75
  loop : -1.42 (0.29), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 203 
 HIS   0.005   0.001   HIS A1403 
 PHE   0.034   0.001   PHE A 625 
 TYR   0.016   0.001   TYR A1342 
 ARG   0.005   0.000   ARG A 304 

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

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

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 180
  time to evaluate  : 1.100 
Fit side-chains
REVERT: A   51 GLU cc_start: 0.9079 (pp20) cc_final: 0.8737 (pp20)
REVERT: A  208 GLN cc_start: 0.7679 (tm-30) cc_final: 0.7435 (tm-30)
REVERT: A  304 ARG cc_start: 0.8430 (ttt-90) cc_final: 0.7914 (ttt-90)
REVERT: A  491 SER cc_start: 0.9366 (OUTLIER) cc_final: 0.8879 (p)
REVERT: A  977 THR cc_start: 0.8798 (OUTLIER) cc_final: 0.8466 (m)
REVERT: A  999 MET cc_start: 0.8218 (tpt) cc_final: 0.7994 (mmm)
REVERT: A 1265 ASP cc_start: 0.8511 (m-30) cc_final: 0.8295 (m-30)
REVERT: A 1322 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8577 (mt-10)
REVERT: A 1406 GLU cc_start: 0.8108 (pt0) cc_final: 0.7629 (tm-30)
REVERT: A 1416 MET cc_start: 0.8608 (tmm) cc_final: 0.7203 (tmm)
REVERT: A 1417 MET cc_start: 0.8635 (ttm) cc_final: 0.7808 (ttt)
REVERT: A 1418 ASP cc_start: 0.8036 (t0) cc_final: 0.7783 (t0)
REVERT: A 1437 HIS cc_start: 0.8275 (m-70) cc_final: 0.7815 (m-70)
  outliers start: 31
  outliers final: 21
  residues processed: 199
  average time/residue: 0.2118
  time to fit residues: 60.1260
Evaluate side-chains
  189 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 166
  time to evaluate  : 1.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 ASN
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  224 SER
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain A residue  452 MET
Chi-restraints excluded: chain A residue  481 ILE
Chi-restraints excluded: chain A residue  491 SER
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  977 THR
Chi-restraints excluded: chain A residue  990 THR
Chi-restraints excluded: chain A residue 1028 THR
Chi-restraints excluded: chain A residue 1030 LEU
Chi-restraints excluded: chain A residue 1092 THR
Chi-restraints excluded: chain A residue 1102 SER
Chi-restraints excluded: chain A residue 1217 THR
Chi-restraints excluded: chain A residue 1408 LEU
Chi-restraints excluded: chain A residue 1423 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 25 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   chunk 93 optimal weight:    4.9990
   chunk 99 optimal weight:    1.9990
   chunk 103 optimal weight:    0.6980
   chunk 30 optimal weight:    3.9990
   chunk 12 optimal weight:    0.8980
   chunk 9 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   chunk 104 optimal weight:    1.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A 853 ASN
A1046 GLN
A1304 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.132621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.110040 restraints weight = 19053.905|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 3.33
r_work: 0.3303 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3312
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3312 r_free = 0.3312    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3312 r_free = 0.3312    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3312
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.9483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9597  Z= 0.244
  Angle     :  0.634   9.297  12985  Z= 0.314
  Chirality :  0.040   0.191   1490
  Planarity :  0.004   0.083   1589
  Dihedral  :  6.696  83.283   1335
  Min Nonbonded Distance : 1.883

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.18 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 23.22 %
    Favored  : 73.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.18 (0.24), residues: 1163
  helix:  1.03 (0.19), residues: 739
  sheet: -0.92 (0.62), residues: 65
  loop : -1.56 (0.29), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 203 
 HIS   0.008   0.001   HIS A1403 
 PHE   0.032   0.001   PHE A 625 
 TYR   0.012   0.001   TYR A 927 
 ARG   0.005   0.001   ARG A 304 

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

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

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 173
  time to evaluate  : 1.077 
Fit side-chains
REVERT: A   51 GLU cc_start: 0.9090 (pp20) cc_final: 0.8744 (pp20)
REVERT: A  138 LEU cc_start: 0.9048 (mp) cc_final: 0.8331 (tp)
REVERT: A  208 GLN cc_start: 0.7786 (tm-30) cc_final: 0.7432 (tm-30)
REVERT: A  491 SER cc_start: 0.9412 (OUTLIER) cc_final: 0.8931 (p)
REVERT: A  977 THR cc_start: 0.8820 (OUTLIER) cc_final: 0.8489 (m)
REVERT: A  999 MET cc_start: 0.8231 (tpt) cc_final: 0.8013 (mmm)
REVERT: A 1046 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8396 (tt0)
REVERT: A 1265 ASP cc_start: 0.8499 (m-30) cc_final: 0.8285 (m-30)
REVERT: A 1322 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8596 (mt-10)
REVERT: A 1406 GLU cc_start: 0.8183 (pt0) cc_final: 0.7777 (tm-30)
REVERT: A 1416 MET cc_start: 0.8697 (tmm) cc_final: 0.7237 (tmm)
REVERT: A 1417 MET cc_start: 0.8615 (ttm) cc_final: 0.7736 (ttt)
REVERT: A 1418 ASP cc_start: 0.7994 (t0) cc_final: 0.7710 (t0)
REVERT: A 1437 HIS cc_start: 0.8366 (m-70) cc_final: 0.7890 (m-70)
  outliers start: 32
  outliers final: 24
  residues processed: 194
  average time/residue: 0.2093
  time to fit residues: 57.7204
Evaluate side-chains
  192 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 165
  time to evaluate  : 0.985 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  133 THR
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  224 SER
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  326 HIS
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain A residue  452 MET
Chi-restraints excluded: chain A residue  481 ILE
Chi-restraints excluded: chain A residue  491 SER
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  977 THR
Chi-restraints excluded: chain A residue  990 THR
Chi-restraints excluded: chain A residue 1013 ILE
Chi-restraints excluded: chain A residue 1028 THR
Chi-restraints excluded: chain A residue 1030 LEU
Chi-restraints excluded: chain A residue 1046 GLN
Chi-restraints excluded: chain A residue 1092 THR
Chi-restraints excluded: chain A residue 1102 SER
Chi-restraints excluded: chain A residue 1217 THR
Chi-restraints excluded: chain A residue 1360 SER
Chi-restraints excluded: chain A residue 1408 LEU
Chi-restraints excluded: chain A residue 1423 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 96 optimal weight:    0.2980
   chunk 59 optimal weight:    0.9990
   chunk 48 optimal weight:    0.8980
   chunk 95 optimal weight:    0.4980
   chunk 81 optimal weight:    0.8980
   chunk 112 optimal weight:    0.9980
   chunk 5 optimal weight:    0.5980
   chunk 0 optimal weight:    7.9990
   chunk 108 optimal weight:    0.8980
   chunk 109 optimal weight:    0.9980
   chunk 54 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 853 ASN
A1046 GLN
A1047 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.135450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.112914 restraints weight = 18537.187|
|-----------------------------------------------------------------------------|
r_work (start): 0.3479 rms_B_bonded: 3.26
r_work: 0.3353 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3348
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3348 r_free = 0.3348    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3348 r_free = 0.3348    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.63   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3348
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.9628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9597  Z= 0.180
  Angle     :  0.625   8.927  12985  Z= 0.308
  Chirality :  0.040   0.187   1490
  Planarity :  0.004   0.090   1589
  Dihedral  :  6.600  82.221   1335
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.75 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 24.80 %
    Favored  : 72.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.24), residues: 1163
  helix:  1.14 (0.19), residues: 737
  sheet: -0.80 (0.61), residues: 65
  loop : -1.53 (0.29), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 203 
 HIS   0.003   0.001   HIS A 200 
 PHE   0.033   0.001   PHE A 625 
 TYR   0.010   0.001   TYR A1342 
 ARG   0.007   0.000   ARG A 304 

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

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

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 183
  time to evaluate  : 1.141 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.7814 (mtp85) cc_final: 0.6892 (ttp-170)
REVERT: A   51 GLU cc_start: 0.9081 (pp20) cc_final: 0.8734 (pp20)
REVERT: A  138 LEU cc_start: 0.8966 (mp) cc_final: 0.8214 (tp)
REVERT: A  208 GLN cc_start: 0.7690 (tm-30) cc_final: 0.7383 (tm-30)
REVERT: A  451 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7690 (mt-10)
REVERT: A  940 PHE cc_start: 0.7827 (m-80) cc_final: 0.7624 (m-80)
REVERT: A  977 THR cc_start: 0.8751 (OUTLIER) cc_final: 0.8423 (m)
REVERT: A 1322 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8439 (mt-10)
REVERT: A 1406 GLU cc_start: 0.8180 (pt0) cc_final: 0.7798 (tm-30)
REVERT: A 1416 MET cc_start: 0.8558 (tmm) cc_final: 0.7178 (tmm)
REVERT: A 1417 MET cc_start: 0.8540 (ttm) cc_final: 0.7688 (ttt)
REVERT: A 1418 ASP cc_start: 0.8040 (t0) cc_final: 0.7767 (t0)
REVERT: A 1437 HIS cc_start: 0.8304 (m-70) cc_final: 0.7822 (m-70)
REVERT: A 1446 GLU cc_start: 0.8302 (pp20) cc_final: 0.7608 (tm-30)
  outliers start: 24
  outliers final: 18
  residues processed: 200
  average time/residue: 0.2094
  time to fit residues: 60.0907
Evaluate side-chains
  187 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 168
  time to evaluate  : 1.026 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  224 SER
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  326 HIS
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain A residue  452 MET
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  977 THR
Chi-restraints excluded: chain A residue  990 THR
Chi-restraints excluded: chain A residue 1028 THR
Chi-restraints excluded: chain A residue 1030 LEU
Chi-restraints excluded: chain A residue 1092 THR
Chi-restraints excluded: chain A residue 1102 SER
Chi-restraints excluded: chain A residue 1217 THR
Chi-restraints excluded: chain A residue 1408 LEU
Chi-restraints excluded: chain A residue 1423 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 14 optimal weight:    0.6980
   chunk 13 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 11 optimal weight:    8.9990
   chunk 60 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   chunk 82 optimal weight:    1.9990
   chunk 79 optimal weight:    0.5980
   chunk 109 optimal weight:    1.9990
   overall best weight:    1.0586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.133293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.110784 restraints weight = 18824.367|
|-----------------------------------------------------------------------------|
r_work (start): 0.3457 rms_B_bonded: 3.28
r_work: 0.3332 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3327
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3327 r_free = 0.3327    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.63   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3327 r_free = 0.3327    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.65   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3327
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.9820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   9597  Z= 0.225
  Angle     :  0.655   8.847  12985  Z= 0.323
  Chirality :  0.040   0.181   1490
  Planarity :  0.004   0.091   1589
  Dihedral  :  6.631  82.207   1335
  Min Nonbonded Distance : 1.896

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.27 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 25.10 %
    Favored  : 72.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.24), residues: 1163
  helix:  1.05 (0.19), residues: 746
  sheet: -0.86 (0.62), residues: 65
  loop : -1.55 (0.29), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 203 
 HIS   0.004   0.001   HIS A 608 
 PHE   0.032   0.001   PHE A 625 
 TYR   0.014   0.001   TYR A 927 
 ARG   0.007   0.001   ARG A 336 

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

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

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2326 Ramachandran restraints generated.
    1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 178
  time to evaluate  : 1.178 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.7803 (mtp85) cc_final: 0.6880 (ttp-170)
REVERT: A   51 GLU cc_start: 0.9059 (pp20) cc_final: 0.8715 (pp20)
REVERT: A  138 LEU cc_start: 0.9000 (mp) cc_final: 0.8316 (tp)
REVERT: A  208 GLN cc_start: 0.7825 (tm-30) cc_final: 0.7455 (tm-30)
REVERT: A  293 GLU cc_start: 0.8496 (tt0) cc_final: 0.8155 (tt0)
REVERT: A  345 MET cc_start: 0.8520 (mtt) cc_final: 0.8189 (mmp)
REVERT: A  451 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7691 (mt-10)
REVERT: A  491 SER cc_start: 0.9349 (OUTLIER) cc_final: 0.8863 (p)
REVERT: A  977 THR cc_start: 0.8755 (OUTLIER) cc_final: 0.8413 (m)
REVERT: A 1308 TYR cc_start: 0.7836 (m-10) cc_final: 0.7614 (m-10)
REVERT: A 1322 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8505 (mt-10)
REVERT: A 1406 GLU cc_start: 0.8341 (pt0) cc_final: 0.7941 (tm-30)
REVERT: A 1416 MET cc_start: 0.8614 (tmm) cc_final: 0.7185 (tmm)
REVERT: A 1417 MET cc_start: 0.8592 (ttm) cc_final: 0.7741 (ttt)
REVERT: A 1418 ASP cc_start: 0.8107 (t0) cc_final: 0.7840 (t0)
REVERT: A 1428 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.8269 (mm)
REVERT: A 1437 HIS cc_start: 0.8443 (m-70) cc_final: 0.7950 (m-70)
REVERT: A 1446 GLU cc_start: 0.8271 (pp20) cc_final: 0.7632 (tm-30)
  outliers start: 24
  outliers final: 20
  residues processed: 192
  average time/residue: 0.2034
  time to fit residues: 56.4274
Evaluate side-chains
  194 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 171
  time to evaluate  : 1.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 GLN
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  224 SER
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  326 HIS
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain A residue  452 MET
Chi-restraints excluded: chain A residue  491 SER
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  977 THR
Chi-restraints excluded: chain A residue  990 THR
Chi-restraints excluded: chain A residue 1028 THR
Chi-restraints excluded: chain A residue 1030 LEU
Chi-restraints excluded: chain A residue 1092 THR
Chi-restraints excluded: chain A residue 1102 SER
Chi-restraints excluded: chain A residue 1231 LEU
Chi-restraints excluded: chain A residue 1360 SER
Chi-restraints excluded: chain A residue 1408 LEU
Chi-restraints excluded: chain A residue 1423 LYS
Chi-restraints excluded: chain A residue 1428 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 42 optimal weight:    5.9990
   chunk 99 optimal weight:    0.7980
   chunk 102 optimal weight:    4.9990
   chunk 110 optimal weight:    4.9990
   chunk 44 optimal weight:    3.9990
   chunk 106 optimal weight:    3.9990
   chunk 111 optimal weight:    3.9990
   chunk 6 optimal weight:    0.6980
   chunk 77 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 80 optimal weight:    0.6980
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.133291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.110831 restraints weight = 18684.063|
|-----------------------------------------------------------------------------|
r_work (start): 0.3452 rms_B_bonded: 3.26
r_work: 0.3325 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3323
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3323 r_free = 0.3323    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.65   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3323 r_free = 0.3323    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.67   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3323
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.9958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9597  Z= 0.226
  Angle     :  0.667  10.554  12985  Z= 0.326
  Chirality :  0.040   0.190   1490
  Planarity :  0.004   0.087   1589
  Dihedral  :  6.648  83.393   1335
  Min Nonbonded Distance : 1.897

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.10 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 25.10 %
    Favored  : 72.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.24), residues: 1163
  helix:  1.02 (0.19), residues: 746
  sheet: -0.88 (0.61), residues: 65
  loop : -1.53 (0.29), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 203 
 HIS   0.004   0.001   HIS A 608 
 PHE   0.031   0.001   PHE A 625 
 TYR   0.011   0.001   TYR A 927 
 ARG   0.010   0.001   ARG A 304 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4731.79 seconds
wall clock time: 85 minutes 9.49 seconds (5109.49 seconds total)