Starting phenix.real_space_refine
on Thu Jun 19 11:30:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jy4_36719/06_2025/8jy4_36719.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jy4_36719/06_2025/8jy4_36719.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.58
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jy4_36719/06_2025/8jy4_36719.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jy4_36719/06_2025/8jy4_36719.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jy4_36719/06_2025/8jy4_36719.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jy4_36719/06_2025/8jy4_36719.cif"
  }
  resolution = 3.58
  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=   0.007 sd=   0.053
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: 5
    Type Number    sf(0)   Gaussians
     S      57      5.16       5
     C    7139      2.51       5
     N    1820      2.21       5
     O    1978      1.98       5
     H   11252      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 41 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 22246
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 22246
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1383, 22246
          Classifications: {'peptide': 1383}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 1339}
          Chain breaks: 3
  Time building chain proxies: 9.62, per 1000 atoms: 0.43
  Number of scatterers: 22246
  At special positions: 0
  Unit cell: (104.86, 128.4, 146.59, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      57     16.00
     O    1978      8.00
     N    1820      7.00
     C    7139      6.00
     H   11252      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   6 " - pdb=" SG  CYS A  26 " distance=2.03

  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: 5.44
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2618

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 6 sheets defined
      70.4% alpha, 5.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.84
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 17
      removed outlier: 3.606A  pdb=" N   ASP A  17 " --> pdb=" O   SER A  14 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 24 through 31
    Processing helix  chain 'A' and resid 33 through 44
    Processing helix  chain 'A' and resid 45 through 54
      removed outlier: 4.583A  pdb=" N   VAL A  51 " --> pdb=" O   GLN A  47 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   SER A  54 " --> pdb=" O   HIS A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 88
      removed outlier: 3.609A  pdb=" N   LEU A  66 " --> pdb=" O   THR A  62 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   VAL A  72 " --> pdb=" O   LYS A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 121
      removed outlier: 3.690A  pdb=" N   TYR A 101 " --> pdb=" O   PRO A  97 " (cutoff:3.500A)
      Proline residue:  A 104  - end of helix
    Processing helix  chain 'A' and resid 129 through 157
      removed outlier: 3.549A  pdb=" N   ILE A 137 " --> pdb=" O   SER A 133 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   CYS A 142 " --> pdb=" O   LEU A 138 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   GLY A 143 " --> pdb=" O   SER A 139 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   PHE A 145 " --> pdb=" O   LEU A 141 " (cutoff:3.500A)
      removed outlier: 5.167A  pdb=" N   GLN A 146 " --> pdb=" O   CYS A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 161 through 184
      removed outlier: 3.651A  pdb=" N   LEU A 167 " --> pdb=" O   ALA A 163 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   PHE A 184 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 205
      removed outlier: 3.831A  pdb=" N   THR A 205 " --> pdb=" O   LEU A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 208
      No H-bonds generated for 'chain 'A' and resid 206 through 208'
    Processing helix  chain 'A' and resid 209 through 216
    Processing helix  chain 'A' and resid 222 through 226
      removed outlier: 3.514A  pdb=" N   VAL A 226 " --> pdb=" O   LEU A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 266
      removed outlier: 3.609A  pdb=" N   HIS A 245 " --> pdb=" O   LYS A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 334
      removed outlier: 7.335A  pdb=" N   MET A 320 " --> pdb=" O   LYS A 316 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   VAL A 321 " --> pdb=" O   THR A 317 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   SER A 325 " --> pdb=" O   VAL A 321 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   PHE A 326 " --> pdb=" O   LEU A 322 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   LEU A 328 " --> pdb=" O   LYS A 324 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   LEU A 330 " --> pdb=" O   PHE A 326 " (cutoff:3.500A)
      removed outlier: 4.811A  pdb=" N   VAL A 331 " --> pdb=" O   LEU A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 351
      removed outlier: 3.823A  pdb=" N   GLN A 341 " --> pdb=" O   PHE A 337 " (cutoff:3.500A)
      removed outlier: 4.281A  pdb=" N   LEU A 345 " --> pdb=" O   GLN A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 405
      removed outlier: 3.875A  pdb=" N   GLY A 360 " --> pdb=" O   TYR A 356 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   ALA A 371 " --> pdb=" O   LEU A 367 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   GLN A 374 " --> pdb=" O   ALA A 370 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   TYR A 381 " --> pdb=" O   CYS A 377 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   LEU A 384 " --> pdb=" O   CYS A 380 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   LEU A 388 " --> pdb=" O   LEU A 384 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   GLY A 389 " --> pdb=" O   CYS A 385 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ALA A 395 " --> pdb=" O   LYS A 391 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   SER A 399 " --> pdb=" O   ALA A 395 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   TYR A 401 " --> pdb=" O   MET A 397 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   LYS A 402 " --> pdb=" O   ALA A 398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 408 through 413
    Processing helix  chain 'A' and resid 416 through 423
      removed outlier: 3.674A  pdb=" N   ASN A 422 " --> pdb=" O   GLY A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 437
      removed outlier: 3.567A  pdb=" N   ASP A 433 " --> pdb=" O   GLN A 429 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   PHE A 437 " --> pdb=" O   ASP A 433 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 441
    Processing helix  chain 'A' and resid 442 through 460
      removed outlier: 3.584A  pdb=" N   GLU A 458 " --> pdb=" O   PHE A 454 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 508
      removed outlier: 3.873A  pdb=" N   GLY A 466 " --> pdb=" O   SER A 462 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   MET A 470 " --> pdb=" O   GLY A 466 " (cutoff:3.500A)
      Proline residue:  A 475  - end of helix
      removed outlier: 4.060A  pdb=" N   LYS A 493 " --> pdb=" O   VAL A 489 " (cutoff:3.500A)
      removed outlier: 4.568A  pdb=" N   ASN A 494 " --> pdb=" O   LYS A 490 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   SER A 507 " --> pdb=" O   ASN A 503 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 508 through 515
      removed outlier: 3.555A  pdb=" N   PHE A 515 " --> pdb=" O   ILE A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 517 through 552
      removed outlier: 3.699A  pdb=" N   PHE A 521 " --> pdb=" O   TRP A 517 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   ASN A 535 " --> pdb=" O   LYS A 531 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   ALA A 538 " --> pdb=" O   LYS A 534 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   VAL A 546 " --> pdb=" O   LEU A 542 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 552 through 569
      removed outlier: 3.668A  pdb=" N   SER A 558 " --> pdb=" O   PRO A 554 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   VAL A 559 " --> pdb=" O   VAL A 555 " (cutoff:3.500A)
      removed outlier: 4.443A  pdb=" N   VAL A 566 " --> pdb=" O   PHE A 562 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   ASP A 569 " --> pdb=" O   TYR A 565 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 575 through 581
    Processing helix  chain 'A' and resid 582 through 618
      removed outlier: 3.733A  pdb=" N   ASN A 587 " --> pdb=" O   ILE A 583 " (cutoff:3.500A)
      removed outlier: 4.771A  pdb=" N   PHE A 591 " --> pdb=" O   ASN A 587 " (cutoff:3.500A)
      Proline residue:  A 592  - end of helix
      Proline residue:  A 597  - end of helix
      removed outlier: 3.812A  pdb=" N   SER A 601 " --> pdb=" O   PRO A 597 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   SER A 602 " --> pdb=" O   MET A 598 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   SER A 607 " --> pdb=" O   MET A 603 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   VAL A 608 " --> pdb=" O   LEU A 604 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   GLU A 611 " --> pdb=" O   SER A 607 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   LEU A 613 " --> pdb=" O   SER A 609 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 678 through 686
    Processing helix  chain 'A' and resid 714 through 721
    Processing helix  chain 'A' and resid 726 through 737
    Processing helix  chain 'A' and resid 738 through 746
      removed outlier: 3.774A  pdb=" N   ASP A 742 " --> pdb=" O   ALA A 738 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   GLU A 744 " --> pdb=" O   LEU A 740 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   MET A 745 " --> pdb=" O   PRO A 741 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   LEU A 746 " --> pdb=" O   ASP A 742 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 762 through 778
      removed outlier: 3.673A  pdb=" N   ASN A 778 " --> pdb=" O   ALA A 774 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 792 through 803
    Processing helix  chain 'A' and resid 824 through 828
    Processing helix  chain 'A' and resid 848 through 852
      removed outlier: 3.626A  pdb=" N   LYS A 851 " --> pdb=" O   LEU A 848 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   LYS A 852 " --> pdb=" O   LEU A 849 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 848 through 852'
    Processing helix  chain 'A' and resid 964 through 975
    Processing helix  chain 'A' and resid 975 through 1005
      removed outlier: 3.619A  pdb=" N   PHE A 981 " --> pdb=" O   PHE A 977 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1006 through 1009
    Processing helix  chain 'A' and resid 1016 through 1065
      removed outlier: 3.800A  pdb=" N   GLN A1034 " --> pdb=" O   LEU A1030 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   GLY A1035 " --> pdb=" O   GLY A1031 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   ALA A1041 " --> pdb=" O   PHE A1037 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   TRP A1044 " --> pdb=" O   ILE A1040 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   HIS A1057 " --> pdb=" O   SER A1053 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   LYS A1058 " --> pdb=" O   ASN A1054 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LEU A1061 " --> pdb=" O   HIS A1057 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1068 through 1075
      removed outlier: 3.841A  pdb=" N   PHE A1072 " --> pdb=" O   PRO A1068 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1076 through 1084
      removed outlier: 3.966A  pdb=" N   ILE A1080 " --> pdb=" O   PRO A1076 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1086 through 1094
      removed outlier: 4.008A  pdb=" N   ASP A1092 " --> pdb=" O   ILE A1088 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   THR A1094 " --> pdb=" O   THR A1090 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1094 through 1118
      removed outlier: 4.102A  pdb=" N   SER A1101 " --> pdb=" O   GLN A1097 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   GLY A1108 " --> pdb=" O   THR A1104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1122 through 1168
      removed outlier: 4.021A  pdb=" N   ILE A1126 " --> pdb=" O   VAL A1122 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   ILE A1128 " --> pdb=" O   THR A1124 " (cutoff:3.500A)
      Proline residue:  A1129  - end of helix
      removed outlier: 3.748A  pdb=" N   PHE A1140 " --> pdb=" O   SER A1136 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   SER A1143 " --> pdb=" O   MET A1139 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ARG A1146 " --> pdb=" O   VAL A1142 " (cutoff:3.500A)
      removed outlier: 4.878A  pdb=" N   GLN A1147 " --> pdb=" O   SER A1143 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   SER A1157 " --> pdb=" O   SER A1153 " (cutoff:3.500A)
      Proline residue:  A1158  - end of helix
    Processing helix  chain 'A' and resid 1169 through 1177
      removed outlier: 3.667A  pdb=" N   ILE A1173 " --> pdb=" O   GLY A1169 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ALA A1175 " --> pdb=" O   PRO A1171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1178 through 1213
      removed outlier: 3.732A  pdb=" N   VAL A1188 " --> pdb=" O   LYS A1184 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   ARG A1189 " --> pdb=" O   HIS A1185 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   THR A1192 " --> pdb=" O   VAL A1188 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ASN A1193 " --> pdb=" O   ARG A1189 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   CYS A1196 " --> pdb=" O   THR A1192 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   SER A1199 " --> pdb=" O   LYS A1195 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   SER A1203 " --> pdb=" O   SER A1199 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   LEU A1207 " --> pdb=" O   SER A1203 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   ALA A1208 " --> pdb=" O   ASN A1204 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   ARG A1210 " --> pdb=" O   TRP A1206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1213 through 1229
      removed outlier: 3.973A  pdb=" N   VAL A1219 " --> pdb=" O   GLY A1215 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   SER A1222 " --> pdb=" O   THR A1218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1236 through 1246
      removed outlier: 3.961A  pdb=" N   PHE A1240 " --> pdb=" O   ASP A1236 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   VAL A1241 " --> pdb=" O   THR A1237 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ALA A1245 " --> pdb=" O   VAL A1241 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   LEU A1246 " --> pdb=" O   LEU A1242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1247 through 1266
      removed outlier: 3.976A  pdb=" N   ASN A1253 " --> pdb=" O   THR A1249 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   TRP A1254 " --> pdb=" O   GLN A1250 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   VAL A1256 " --> pdb=" O   LEU A1252 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   THR A1259 " --> pdb=" O   LEU A1255 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   GLU A1261 " --> pdb=" O   ARG A1257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1266 through 1277
      removed outlier: 3.682A  pdb=" N   TYR A1275 " --> pdb=" O   ARG A1271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1339 through 1348
      removed outlier: 3.590A  pdb=" N   THR A1344 " --> pdb=" O   LYS A1340 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   PHE A1348 " --> pdb=" O   THR A1344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1366 through 1368
      No H-bonds generated for 'chain 'A' and resid 1366 through 1368'
    Processing helix  chain 'A' and resid 1369 through 1375
    Processing helix  chain 'A' and resid 1391 through 1396
    Processing helix  chain 'A' and resid 1402 through 1413
    Processing helix  chain 'A' and resid 1415 through 1422
    Processing helix  chain 'A' and resid 1424 through 1427
    Processing helix  chain 'A' and resid 1431 through 1435
    Processing helix  chain 'A' and resid 1438 through 1454
    Processing helix  chain 'A' and resid 1468 through 1483
    Processing helix  chain 'A' and resid 1494 through 1498
    Processing helix  chain 'A' and resid 1517 through 1524
    Processing helix  chain 'A' and resid 1526 through 1533
    Processing sheet with id=AA1, first strand: chain 'A' and resid 627 through 629
      removed outlier: 6.189A  pdb=" N   ARG A 628 " --> pdb=" O   ILE A 697 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 654 through 657
      removed outlier: 5.440A  pdb=" N   ALA A 642 " --> pdb=" O   ASP A 656 " (cutoff:3.500A)
      removed outlier: 6.957A  pdb=" N   SER A 643 " --> pdb=" O   VAL A 691 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   GLU A 689 " --> pdb=" O   THR A 645 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 701 through 703
      removed outlier: 6.176A  pdb=" N   ALA A 702 " --> pdb=" O   LEU A 783 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   GLU A 830 " --> pdb=" O   LEU A 666 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1317 through 1324
      removed outlier: 7.256A  pdb=" N   ARG A1318 " --> pdb=" O   GLN A1306 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   GLN A1306 " --> pdb=" O   ARG A1318 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   ILE A1320 " --> pdb=" O   ASN A1304 " (cutoff:3.500A)
      removed outlier: 5.387A  pdb=" N   PHE A1302 " --> pdb=" O   ILE A1359 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   ILE A1359 " --> pdb=" O   PHE A1302 " (cutoff:3.500A)
      removed outlier: 5.372A  pdb=" N   ASN A1304 " --> pdb=" O   GLN A1357 " (cutoff:3.500A)
      removed outlier: 5.033A  pdb=" N   GLN A1357 " --> pdb=" O   ASN A1304 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1377 through 1380
      removed outlier: 6.471A  pdb=" N   LYS A1329 " --> pdb=" O   LYS A1503 " (cutoff:3.500A)
      removed outlier: 7.849A  pdb=" N   MET A1505 " --> pdb=" O   LYS A1329 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   GLY A1331 " --> pdb=" O   MET A1505 " (cutoff:3.500A)
      removed outlier: 7.467A  pdb=" N   LEU A1507 " --> pdb=" O   GLY A1331 " (cutoff:3.500A)
      removed outlier: 6.221A  pdb=" N   VAL A1333 " --> pdb=" O   LEU A1507 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   GLU A1514 " --> pdb=" O   VAL A1506 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   ASP A1508 " --> pdb=" O   ILE A1512 " (cutoff:3.500A)
      removed outlier: 5.463A  pdb=" N   ILE A1512 " --> pdb=" O   ASP A1508 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1389 through 1390

    638 hydrogen bonds defined for protein.
    1860 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: 10.85

  Time building geometry restraints manager: 6.78 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 11234
        1.03 -     1.23: 19
        1.23 -     1.42: 4631
        1.42 -     1.62: 6502
        1.62 -     1.81: 94
  Bond restraints: 22480
  Sorted by residual:
  bond pdb=" CA  PHE A1084 "
       pdb=" CB  PHE A1084 "
    ideal  model  delta    sigma   weight residual
    1.528  1.545 -0.017 1.35e-02 5.49e+03 1.61e+00
  bond pdb=" CA  ASP A 786 "
       pdb=" CB  ASP A 786 "
    ideal  model  delta    sigma   weight residual
    1.522  1.530 -0.007 7.00e-03 2.04e+04 1.10e+00
  bond pdb=" CA  CYS A 142 "
       pdb=" C   CYS A 142 "
    ideal  model  delta    sigma   weight residual
    1.523  1.508  0.014 1.41e-02 5.03e+03 1.05e+00
  bond pdb=" CA  ASP A 786 "
       pdb=" C   ASP A 786 "
    ideal  model  delta    sigma   weight residual
    1.531  1.524  0.008 7.40e-03 1.83e+04 1.03e+00
  bond pdb=" CB  TRP A  46 "
       pdb=" CG  TRP A  46 "
    ideal  model  delta    sigma   weight residual
    1.498  1.528 -0.030 3.10e-02 1.04e+03 9.39e-01
  ... (remaining 22475 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.11: 38153
        1.11 -     2.22: 2395
        2.22 -     3.33: 126
        3.33 -     4.45: 41
        4.45 -     5.56: 5
  Bond angle restraints: 40720
  Sorted by residual:
  angle pdb=" N   VAL A 840 "
        pdb=" CA  VAL A 840 "
        pdb=" C   VAL A 840 "
      ideal   model   delta    sigma   weight residual
     111.62  109.07    2.55 7.90e-01 1.60e+00 1.05e+01
  angle pdb=" N   LYS A 757 "
        pdb=" CA  LYS A 757 "
        pdb=" CB  LYS A 757 "
      ideal   model   delta    sigma   weight residual
     114.17  110.52    3.65 1.14e+00 7.69e-01 1.03e+01
  angle pdb=" N   ILE A1040 "
        pdb=" CA  ILE A1040 "
        pdb=" C   ILE A1040 "
      ideal   model   delta    sigma   weight residual
     112.98  109.39    3.59 1.25e+00 6.40e-01 8.26e+00
  angle pdb=" N   PHE A1084 "
        pdb=" CA  PHE A1084 "
        pdb=" C   PHE A1084 "
      ideal   model   delta    sigma   weight residual
     112.26  108.78    3.48 1.32e+00 5.74e-01 6.93e+00
  angle pdb=" N   PHE A1084 "
        pdb=" CA  PHE A1084 "
        pdb=" CB  PHE A1084 "
      ideal   model   delta    sigma   weight residual
     111.17  106.88    4.29 1.64e+00 3.72e-01 6.84e+00
  ... (remaining 40715 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.84: 9302
       17.84 -    35.67: 902
       35.67 -    53.51: 231
       53.51 -    71.35: 60
       71.35 -    89.19: 9
  Dihedral angle restraints: 10504
    sinusoidal: 5686
      harmonic: 4818
  Sorted by residual:
  dihedral pdb=" CB  GLU A 647 "
           pdb=" CG  GLU A 647 "
           pdb=" CD  GLU A 647 "
           pdb=" OE1 GLU A 647 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.19   89.19     1      3.00e+01 1.11e-03 1.05e+01
  dihedral pdb=" CB  GLU A 614 "
           pdb=" CG  GLU A 614 "
           pdb=" CD  GLU A 614 "
           pdb=" OE1 GLU A 614 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.77  -88.77     1      3.00e+01 1.11e-03 1.04e+01
  dihedral pdb=" CA  HIS A 823 "
           pdb=" C   HIS A 823 "
           pdb=" N   PHE A 824 "
           pdb=" CA  PHE A 824 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.55  -15.45     0      5.00e+00 4.00e-02 9.55e+00
  ... (remaining 10501 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 1142
       0.028 -    0.055: 423
       0.055 -    0.083: 135
       0.083 -    0.111: 65
       0.111 -    0.139: 19
  Chirality restraints: 1784
  Sorted by residual:
  chirality pdb=" CB  ILE A 479 "
            pdb=" CA  ILE A 479 "
            pdb=" CG1 ILE A 479 "
            pdb=" CG2 ILE A 479 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.78   -0.14 2.00e-01 2.50e+01 4.80e-01
  chirality pdb=" CA  ILE A1524 "
            pdb=" N   ILE A1524 "
            pdb=" C   ILE A1524 "
            pdb=" CB  ILE A1524 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.70e-01
  chirality pdb=" CA  ILE A 759 "
            pdb=" N   ILE A 759 "
            pdb=" C   ILE A 759 "
            pdb=" CB  ILE A 759 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.48e-01
  ... (remaining 1781 not shown)

  Planarity restraints: 3220
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 746 "    0.033 5.00e-02 4.00e+02   5.03e-02 4.05e+00
        pdb=" N   PRO A 747 "   -0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO A 747 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 747 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A1084 "   -0.010 2.00e-02 2.50e+03   1.91e-02 3.66e+00
        pdb=" C   PHE A1084 "    0.033 2.00e-02 2.50e+03
        pdb=" O   PHE A1084 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   ALA A1085 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A1157 "   -0.025 5.00e-02 4.00e+02   3.82e-02 2.33e+00
        pdb=" N   PRO A1158 "    0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO A1158 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A1158 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 3217 not shown)

  Histogram of nonbonded interaction distances:
        1.57 -     2.18: 1097
        2.18 -     2.78: 45268
        2.78 -     3.39: 62741
        3.39 -     3.99: 77298
        3.99 -     4.60: 121616
  Nonbonded interactions: 308020
  Sorted by model distance:
  nonbonded pdb=" O   PHE A 800 "
            pdb=" H   GLY A 805 "
     model   vdw
     1.573 2.450
  nonbonded pdb=" OE1 GLN A 707 "
            pdb=" H   GLN A 707 "
     model   vdw
     1.581 2.450
  nonbonded pdb="HD21 ASN A 712 "
            pdb=" OE1 GLU A1165 "
     model   vdw
     1.590 2.450
  nonbonded pdb=" O   LEU A1211 "
            pdb=" H   GLY A1215 "
     model   vdw
     1.610 2.450
  nonbonded pdb=" O   ALA A1002 "
            pdb="HH21 ARG A1023 "
     model   vdw
     1.649 2.450
  ... (remaining 308015 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             0.610
  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:             0.350
  Extract box with map and model:          0.750
  Check model and map are aligned:         0.140
  Set scattering table:                    0.180
  Process input model:                     49.120
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.080
  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:3.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   54.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11229  Z= 0.140
  Angle     :  0.551   5.557  15227  Z= 0.320
  Chirality :  0.037   0.139   1784
  Planarity :  0.003   0.050   1887
  Dihedral  : 15.961  89.185   4073
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.98 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 20.77 %
    Favored  : 79.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    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: -0.52 (0.23), residues: 1375
  helix: -0.21 (0.18), residues: 864
  sheet:  0.29 (0.57), residues: 90
  loop : -0.41 (0.32), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 358 
 HIS   0.002   0.001   HIS A 692 
 PHE   0.009   0.001   PHE A1240 
 TYR   0.010   0.001   TYR A 206 
 ARG   0.004   0.000   ARG A 393 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.25396 (  638)
  hydrogen bonds       : angle       9.24377 ( 1860)
  SS BOND              : bond        0.00026 (    1)
  SS BOND              : angle       0.37120 (    2)
  covalent geometry    : bond        0.00285 (11228)
  covalent geometry    : angle       0.55068 (15225)

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

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

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 242
  time to evaluate  : 1.615 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  249 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8348 (mm-30)
REVERT: A  362 LEU cc_start: 0.9336 (tp) cc_final: 0.9121 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 242
  average time/residue: 0.4433
  time to fit residues: 161.5423
Evaluate side-chains
  178 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 1.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 116 optimal weight:    9.9990
   chunk 104 optimal weight:    4.9990
   chunk 58 optimal weight:   20.0000
   chunk 35 optimal weight:    6.9990
   chunk 70 optimal weight:   20.0000
   chunk 55 optimal weight:    0.6980
   chunk 108 optimal weight:    9.9990
   chunk 41 optimal weight:    8.9990
   chunk 65 optimal weight:    6.9990
   chunk 80 optimal weight:   20.0000
   chunk 125 optimal weight:   20.0000
   overall best weight:    5.7388

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

Flipped N/Q/H residues before XYZ refinement:
A 577 GLN
A1097 GLN
A1247 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.052910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.038973 restraints weight = 186606.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.040823 restraints weight = 77161.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.042052 restraints weight = 43589.043|
|-----------------------------------------------------------------------------|
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.2344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  11229  Z= 0.268
  Angle     :  0.700   6.506  15227  Z= 0.386
  Chirality :  0.040   0.140   1784
  Planarity :  0.005   0.048   1887
  Dihedral  :  3.952  15.516   1474
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.71 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 21.25 %
    Favored  : 76.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    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: -0.56 (0.22), residues: 1375
  helix: -0.18 (0.16), residues: 883
  sheet:  0.06 (0.59), residues: 80
  loop : -0.54 (0.32), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  41 
 HIS   0.003   0.001   HIS A 648 
 PHE   0.016   0.002   PHE A1043 
 TYR   0.011   0.001   TYR A 101 
 ARG   0.005   0.001   ARG A1310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06392 (  638)
  hydrogen bonds       : angle       6.02407 ( 1860)
  SS BOND              : bond        0.00225 (    1)
  SS BOND              : angle       0.18080 (    2)
  covalent geometry    : bond        0.00511 (11228)
  covalent geometry    : angle       0.69976 (15225)

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

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

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 177
  time to evaluate  : 1.658 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  249 GLU cc_start: 0.9392 (mm-30) cc_final: 0.8985 (mm-30)
REVERT: A  362 LEU cc_start: 0.9608 (tp) cc_final: 0.9371 (tt)
REVERT: A  424 MET cc_start: 0.9596 (ptt) cc_final: 0.9395 (ptt)
REVERT: A  438 MET cc_start: 0.9368 (ppp) cc_final: 0.9157 (tmm)
REVERT: A  513 LYS cc_start: 0.9903 (mmmt) cc_final: 0.9637 (tttt)
REVERT: A 1093 ASP cc_start: 0.9213 (m-30) cc_final: 0.8888 (m-30)
  outliers start: 33
  outliers final: 19
  residues processed: 194
  average time/residue: 0.4960
  time to fit residues: 148.8891
Evaluate side-chains
  173 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 154
  time to evaluate  : 1.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  103 ASN
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  117 ILE
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  142 CYS
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  192 ASN
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  547 ILE
Chi-restraints excluded: chain A residue  589 LEU
Chi-restraints excluded: chain A residue  613 LEU
Chi-restraints excluded: chain A residue  799 ILE
Chi-restraints excluded: chain A residue 1030 LEU
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1157 SER
Chi-restraints excluded: chain A residue 1445 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 63 optimal weight:   20.0000
   chunk 106 optimal weight:    6.9990
   chunk 111 optimal weight:    2.9990
   chunk 113 optimal weight:    1.9990
   chunk 36 optimal weight:    8.9990
   chunk 56 optimal weight:    6.9990
   chunk 15 optimal weight:    6.9990
   chunk 24 optimal weight:    9.9990
   chunk 69 optimal weight:   10.0000
   chunk 45 optimal weight:    9.9990
   overall best weight:    3.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 175 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.053465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.039267 restraints weight = 188493.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.041171 restraints weight = 77858.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.042434 restraints weight = 44111.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.2935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  11229  Z= 0.186
  Angle     :  0.599   7.045  15227  Z= 0.323
  Chirality :  0.038   0.200   1784
  Planarity :  0.004   0.043   1887
  Dihedral  :  3.832  14.792   1474
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.20 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 22.07 %
    Favored  : 75.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    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: -0.24 (0.22), residues: 1375
  helix:  0.18 (0.17), residues: 888
  sheet: -0.11 (0.57), residues: 80
  loop : -0.65 (0.32), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  41 
 HIS   0.003   0.001   HIS A 439 
 PHE   0.012   0.001   PHE A1043 
 TYR   0.011   0.001   TYR A 101 
 ARG   0.003   0.000   ARG A 498 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05636 (  638)
  hydrogen bonds       : angle       5.36708 ( 1860)
  SS BOND              : bond        0.00087 (    1)
  SS BOND              : angle       0.09433 (    2)
  covalent geometry    : bond        0.00357 (11228)
  covalent geometry    : angle       0.59930 (15225)

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

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

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 162
  time to evaluate  : 1.833 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 TYR cc_start: 0.9734 (OUTLIER) cc_final: 0.9359 (m-10)
REVERT: A  387 LYS cc_start: 0.9139 (mtpt) cc_final: 0.8852 (mtpp)
REVERT: A  438 MET cc_start: 0.9396 (ppp) cc_final: 0.9167 (tmm)
REVERT: A 1093 ASP cc_start: 0.9026 (m-30) cc_final: 0.8824 (m-30)
  outliers start: 25
  outliers final: 15
  residues processed: 179
  average time/residue: 0.4231
  time to fit residues: 119.2821
Evaluate side-chains
  166 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 150
  time to evaluate  : 1.878 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  107 TYR
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  117 ILE
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  192 ASN
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain A residue  432 MET
Chi-restraints excluded: chain A residue  476 ILE
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain A residue  799 ILE
Chi-restraints excluded: chain A residue 1030 LEU
Chi-restraints excluded: chain A residue 1395 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 26 optimal weight:    9.9990
   chunk 66 optimal weight:    6.9990
   chunk 35 optimal weight:    7.9990
   chunk 130 optimal weight:   20.0000
   chunk 129 optimal weight:   20.0000
   chunk 133 optimal weight:    5.9990
   chunk 56 optimal weight:    2.9990
   chunk 126 optimal weight:    4.9990
   chunk 83 optimal weight:    3.9990
   chunk 3 optimal weight:    6.9990
   chunk 120 optimal weight:   20.0000
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.053208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.039247 restraints weight = 193598.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.041096 restraints weight = 78721.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.042324 restraints weight = 44474.465|
|-----------------------------------------------------------------------------|
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8278
moved from start:          0.3357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  11229  Z= 0.226
  Angle     :  0.605   7.236  15227  Z= 0.328
  Chirality :  0.038   0.135   1784
  Planarity :  0.004   0.042   1887
  Dihedral  :  3.818  15.905   1474
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.93 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 22.15 %
    Favored  : 74.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    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: -0.08 (0.22), residues: 1375
  helix:  0.34 (0.17), residues: 881
  sheet: -0.22 (0.54), residues: 90
  loop : -0.63 (0.32), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  41 
 HIS   0.003   0.001   HIS A1057 
 PHE   0.011   0.001   PHE A1123 
 TYR   0.012   0.001   TYR A 101 
 ARG   0.002   0.000   ARG A1083 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04954 (  638)
  hydrogen bonds       : angle       5.35291 ( 1860)
  SS BOND              : bond        0.00201 (    1)
  SS BOND              : angle       0.17871 (    2)
  covalent geometry    : bond        0.00429 (11228)
  covalent geometry    : angle       0.60527 (15225)

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

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

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 152
  time to evaluate  : 1.948 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 GLU cc_start: 0.9794 (pt0) cc_final: 0.9514 (tm-30)
REVERT: A  107 TYR cc_start: 0.9727 (OUTLIER) cc_final: 0.9388 (m-10)
REVERT: A  387 LYS cc_start: 0.9161 (mtpt) cc_final: 0.8877 (mtpp)
REVERT: A  438 MET cc_start: 0.9418 (ppp) cc_final: 0.9186 (tmm)
  outliers start: 36
  outliers final: 27
  residues processed: 169
  average time/residue: 0.4260
  time to fit residues: 112.5337
Evaluate side-chains
  176 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 148
  time to evaluate  : 1.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 TRP
Chi-restraints excluded: chain A residue   77 ILE
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  103 ASN
Chi-restraints excluded: chain A residue  107 TYR
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  142 CYS
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  192 ASN
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  396 ILE
Chi-restraints excluded: chain A residue  424 MET
Chi-restraints excluded: chain A residue  432 MET
Chi-restraints excluded: chain A residue  476 ILE
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  561 THR
Chi-restraints excluded: chain A residue  799 ILE
Chi-restraints excluded: chain A residue 1030 LEU
Chi-restraints excluded: chain A residue 1056 LEU
Chi-restraints excluded: chain A residue 1065 LEU
Chi-restraints excluded: chain A residue 1130 LEU
Chi-restraints excluded: chain A residue 1134 TYR
Chi-restraints excluded: chain A residue 1395 LEU
Chi-restraints excluded: chain A residue 1445 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 7 optimal weight:    0.7980
   chunk 56 optimal weight:    2.9990
   chunk 122 optimal weight:   20.0000
   chunk 70 optimal weight:    5.9990
   chunk 19 optimal weight:    6.9990
   chunk 18 optimal weight:    9.9990
   chunk 35 optimal weight:    7.9990
   chunk 36 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 44 optimal weight:    8.9990
   chunk 82 optimal weight:    8.9990
   overall best weight:    4.9588

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

Flipped N/Q/H residues before XYZ refinement:
A 629 HIS
A 638 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.052590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.038658 restraints weight = 195515.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.040506 restraints weight = 81273.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.041711 restraints weight = 46050.890|
|-----------------------------------------------------------------------------|
r_work (final): 0.2950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8307
moved from start:          0.3702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  11229  Z= 0.213
  Angle     :  0.601   8.369  15227  Z= 0.322
  Chirality :  0.038   0.135   1784
  Planarity :  0.004   0.045   1887
  Dihedral  :  3.759  16.661   1474
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.56 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 21.42 %
    Favored  : 75.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    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:  0.09 (0.22), residues: 1375
  helix:  0.56 (0.17), residues: 889
  sheet: -0.26 (0.57), residues: 85
  loop : -0.77 (0.32), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 709 
 HIS   0.002   0.001   HIS A1428 
 PHE   0.011   0.001   PHE A 135 
 TYR   0.011   0.001   TYR A 101 
 ARG   0.003   0.000   ARG A1083 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04610 (  638)
  hydrogen bonds       : angle       5.15228 ( 1860)
  SS BOND              : bond        0.00183 (    1)
  SS BOND              : angle       0.08370 (    2)
  covalent geometry    : bond        0.00407 (11228)
  covalent geometry    : angle       0.60110 (15225)

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

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

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 155
  time to evaluate  : 1.610 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 GLU cc_start: 0.9773 (pt0) cc_final: 0.9504 (tm-30)
REVERT: A  107 TYR cc_start: 0.9705 (OUTLIER) cc_final: 0.9346 (m-10)
REVERT: A  387 LYS cc_start: 0.9202 (mtpt) cc_final: 0.8911 (mtpp)
REVERT: A  438 MET cc_start: 0.9413 (ppp) cc_final: 0.9170 (tmm)
REVERT: A  440 MET cc_start: 0.9286 (mmm) cc_final: 0.8901 (mmm)
REVERT: A  502 MET cc_start: 0.9602 (ttp) cc_final: 0.8777 (ttp)
  outliers start: 35
  outliers final: 28
  residues processed: 173
  average time/residue: 0.3994
  time to fit residues: 108.9338
Evaluate side-chains
  176 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 147
  time to evaluate  : 1.564 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 TRP
Chi-restraints excluded: chain A residue   77 ILE
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  103 ASN
Chi-restraints excluded: chain A residue  107 TYR
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  192 ASN
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  432 MET
Chi-restraints excluded: chain A residue  476 ILE
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  596 LEU
Chi-restraints excluded: chain A residue  799 ILE
Chi-restraints excluded: chain A residue 1056 LEU
Chi-restraints excluded: chain A residue 1065 LEU
Chi-restraints excluded: chain A residue 1113 LEU
Chi-restraints excluded: chain A residue 1130 LEU
Chi-restraints excluded: chain A residue 1134 TYR
Chi-restraints excluded: chain A residue 1347 LEU
Chi-restraints excluded: chain A residue 1395 LEU
Chi-restraints excluded: chain A residue 1445 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 81 optimal weight:    8.9990
   chunk 66 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 134 optimal weight:   20.0000
   chunk 24 optimal weight:   10.0000
   chunk 67 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 101 optimal weight:    5.9990
   chunk 88 optimal weight:    5.9990
   chunk 15 optimal weight:   10.0000
   chunk 21 optimal weight:    9.9990
   overall best weight:    3.9788

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.052828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.038934 restraints weight = 194856.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.040806 restraints weight = 80621.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.042034 restraints weight = 45727.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.3891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11229  Z= 0.177
  Angle     :  0.574   7.166  15227  Z= 0.306
  Chirality :  0.038   0.137   1784
  Planarity :  0.003   0.045   1887
  Dihedral  :  3.699  16.448   1474
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.85 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 21.42 %
    Favored  : 75.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.22), residues: 1375
  helix:  0.84 (0.17), residues: 897
  sheet: -0.23 (0.57), residues: 85
  loop : -0.61 (0.33), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 709 
 HIS   0.002   0.001   HIS A1057 
 PHE   0.024   0.001   PHE A1084 
 TYR   0.011   0.001   TYR A 101 
 ARG   0.003   0.000   ARG A1083 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04426 (  638)
  hydrogen bonds       : angle       4.96392 ( 1860)
  SS BOND              : bond        0.00149 (    1)
  SS BOND              : angle       0.07744 (    2)
  covalent geometry    : bond        0.00346 (11228)
  covalent geometry    : angle       0.57433 (15225)

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

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

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 150
  time to evaluate  : 1.582 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 GLU cc_start: 0.9766 (pt0) cc_final: 0.9500 (tm-30)
REVERT: A  107 TYR cc_start: 0.9689 (OUTLIER) cc_final: 0.9376 (m-10)
REVERT: A  387 LYS cc_start: 0.9217 (mtpt) cc_final: 0.8838 (mtpp)
REVERT: A  438 MET cc_start: 0.9397 (ppp) cc_final: 0.9166 (tmm)
REVERT: A  440 MET cc_start: 0.9218 (mmm) cc_final: 0.8893 (mmm)
  outliers start: 39
  outliers final: 32
  residues processed: 168
  average time/residue: 0.4514
  time to fit residues: 116.9380
Evaluate side-chains
  176 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 143
  time to evaluate  : 1.631 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 TRP
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  103 ASN
Chi-restraints excluded: chain A residue  107 TYR
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  110 THR
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  142 CYS
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  192 ASN
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  396 ILE
Chi-restraints excluded: chain A residue  432 MET
Chi-restraints excluded: chain A residue  476 ILE
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  596 LEU
Chi-restraints excluded: chain A residue  799 ILE
Chi-restraints excluded: chain A residue 1056 LEU
Chi-restraints excluded: chain A residue 1065 LEU
Chi-restraints excluded: chain A residue 1113 LEU
Chi-restraints excluded: chain A residue 1116 ILE
Chi-restraints excluded: chain A residue 1130 LEU
Chi-restraints excluded: chain A residue 1134 TYR
Chi-restraints excluded: chain A residue 1209 ILE
Chi-restraints excluded: chain A residue 1327 MET
Chi-restraints excluded: chain A residue 1347 LEU
Chi-restraints excluded: chain A residue 1395 LEU
Chi-restraints excluded: chain A residue 1445 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 33 optimal weight:    6.9990
   chunk 116 optimal weight:    5.9990
   chunk 84 optimal weight:    5.9990
   chunk 25 optimal weight:    0.6980
   chunk 10 optimal weight:   10.0000
   chunk 44 optimal weight:    4.9990
   chunk 40 optimal weight:    7.9990
   chunk 70 optimal weight:    5.9990
   chunk 16 optimal weight:    9.9990
   chunk 127 optimal weight:   20.0000
   chunk 90 optimal weight:   10.0000
   overall best weight:    4.7388

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.052543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.038714 restraints weight = 197425.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.040550 restraints weight = 81866.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.041743 restraints weight = 46562.901|
|-----------------------------------------------------------------------------|
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
moved from start:          0.4112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  11229  Z= 0.208
  Angle     :  0.591   7.388  15227  Z= 0.317
  Chirality :  0.038   0.148   1784
  Planarity :  0.004   0.047   1887
  Dihedral  :  3.698  16.752   1474
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.85 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 22.48 %
    Favored  : 74.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.22), residues: 1375
  helix:  0.81 (0.17), residues: 900
  sheet: -0.20 (0.55), residues: 90
  loop : -0.59 (0.33), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 709 
 HIS   0.003   0.001   HIS A1057 
 PHE   0.013   0.001   PHE A1123 
 TYR   0.010   0.001   TYR A 101 
 ARG   0.003   0.000   ARG A1083 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04327 (  638)
  hydrogen bonds       : angle       5.03218 ( 1860)
  SS BOND              : bond        0.00185 (    1)
  SS BOND              : angle       0.16540 (    2)
  covalent geometry    : bond        0.00400 (11228)
  covalent geometry    : angle       0.59137 (15225)

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

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

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 146
  time to evaluate  : 1.576 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 GLU cc_start: 0.9767 (pt0) cc_final: 0.9488 (tm-30)
REVERT: A  387 LYS cc_start: 0.9238 (mtpt) cc_final: 0.8876 (mtpp)
REVERT: A  438 MET cc_start: 0.9398 (ppp) cc_final: 0.9165 (tmm)
REVERT: A  440 MET cc_start: 0.9172 (mmm) cc_final: 0.8907 (mmm)
REVERT: A  607 SER cc_start: 0.9563 (t) cc_final: 0.9332 (p)
REVERT: A 1258 MET cc_start: 0.9372 (mmt) cc_final: 0.9162 (mmp)
REVERT: A 1261 GLU cc_start: 0.8790 (mp0) cc_final: 0.8573 (mp0)
REVERT: A 1460 LEU cc_start: 0.9740 (OUTLIER) cc_final: 0.9333 (tt)
REVERT: A 1505 MET cc_start: 0.9184 (mmt) cc_final: 0.8940 (mmt)
  outliers start: 34
  outliers final: 30
  residues processed: 163
  average time/residue: 0.3972
  time to fit residues: 100.5510
Evaluate side-chains
  174 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 143
  time to evaluate  : 1.582 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 TRP
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  103 ASN
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  142 CYS
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  192 ASN
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  396 ILE
Chi-restraints excluded: chain A residue  432 MET
Chi-restraints excluded: chain A residue  476 ILE
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  596 LEU
Chi-restraints excluded: chain A residue  799 ILE
Chi-restraints excluded: chain A residue 1056 LEU
Chi-restraints excluded: chain A residue 1065 LEU
Chi-restraints excluded: chain A residue 1113 LEU
Chi-restraints excluded: chain A residue 1130 LEU
Chi-restraints excluded: chain A residue 1134 TYR
Chi-restraints excluded: chain A residue 1209 ILE
Chi-restraints excluded: chain A residue 1327 MET
Chi-restraints excluded: chain A residue 1347 LEU
Chi-restraints excluded: chain A residue 1395 LEU
Chi-restraints excluded: chain A residue 1445 LEU
Chi-restraints excluded: chain A residue 1460 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 120 optimal weight:    8.9990
   chunk 42 optimal weight:    3.9990
   chunk 53 optimal weight:    7.9990
   chunk 111 optimal weight:    0.9980
   chunk 95 optimal weight:    2.9990
   chunk 41 optimal weight:    4.9990
   chunk 94 optimal weight:    0.9990
   chunk 129 optimal weight:   20.0000
   chunk 57 optimal weight:    7.9990
   chunk 38 optimal weight:    3.9990
   chunk 133 optimal weight:    0.0770
   overall best weight:    1.8144

-------------------------------------------------------------------------------
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 = 0.3371 r_free = 0.3371 target = 0.052936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.039294 restraints weight = 190176.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.041156 restraints weight = 78307.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.042364 restraints weight = 44220.309|
|-----------------------------------------------------------------------------|
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8270
moved from start:          0.4181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11229  Z= 0.122
  Angle     :  0.575   7.770  15227  Z= 0.293
  Chirality :  0.038   0.184   1784
  Planarity :  0.003   0.048   1887
  Dihedral  :  3.620  15.957   1474
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.20 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 22.39 %
    Favored  : 74.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    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:  0.89 (0.23), residues: 1375
  helix:  1.15 (0.17), residues: 899
  sheet: -0.10 (0.55), residues: 90
  loop : -0.40 (0.34), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 456 
 HIS   0.002   0.001   HIS A 439 
 PHE   0.011   0.001   PHE A 337 
 TYR   0.011   0.001   TYR A 319 
 ARG   0.002   0.000   ARG A1083 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04249 (  638)
  hydrogen bonds       : angle       4.68247 ( 1860)
  SS BOND              : bond        0.00068 (    1)
  SS BOND              : angle       0.42106 (    2)
  covalent geometry    : bond        0.00264 (11228)
  covalent geometry    : angle       0.57496 (15225)

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

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

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 157
  time to evaluate  : 1.596 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 GLU cc_start: 0.9750 (pt0) cc_final: 0.9511 (tm-30)
REVERT: A  107 TYR cc_start: 0.9648 (OUTLIER) cc_final: 0.9341 (m-10)
REVERT: A  387 LYS cc_start: 0.9212 (mtpt) cc_final: 0.8849 (mtpp)
REVERT: A  438 MET cc_start: 0.9384 (ppp) cc_final: 0.9142 (tmm)
REVERT: A  440 MET cc_start: 0.9184 (mmm) cc_final: 0.8886 (mmm)
REVERT: A  607 SER cc_start: 0.9573 (t) cc_final: 0.9317 (p)
REVERT: A 1460 LEU cc_start: 0.9734 (OUTLIER) cc_final: 0.9325 (tt)
  outliers start: 38
  outliers final: 32
  residues processed: 174
  average time/residue: 0.3950
  time to fit residues: 107.5461
Evaluate side-chains
  182 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 148
  time to evaluate  : 1.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 TRP
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  103 ASN
Chi-restraints excluded: chain A residue  107 TYR
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  110 THR
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  192 ASN
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  432 MET
Chi-restraints excluded: chain A residue  476 ILE
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  567 LEU
Chi-restraints excluded: chain A residue  596 LEU
Chi-restraints excluded: chain A residue  799 ILE
Chi-restraints excluded: chain A residue  971 LEU
Chi-restraints excluded: chain A residue 1032 LEU
Chi-restraints excluded: chain A residue 1056 LEU
Chi-restraints excluded: chain A residue 1065 LEU
Chi-restraints excluded: chain A residue 1113 LEU
Chi-restraints excluded: chain A residue 1130 LEU
Chi-restraints excluded: chain A residue 1134 TYR
Chi-restraints excluded: chain A residue 1209 ILE
Chi-restraints excluded: chain A residue 1327 MET
Chi-restraints excluded: chain A residue 1347 LEU
Chi-restraints excluded: chain A residue 1395 LEU
Chi-restraints excluded: chain A residue 1445 LEU
Chi-restraints excluded: chain A residue 1460 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 14 optimal weight:    7.9990
   chunk 103 optimal weight:   10.0000
   chunk 46 optimal weight:    7.9990
   chunk 10 optimal weight:    7.9990
   chunk 122 optimal weight:   10.0000
   chunk 13 optimal weight:    0.8980
   chunk 110 optimal weight:    8.9990
   chunk 69 optimal weight:   10.0000
   chunk 114 optimal weight:    0.6980
   chunk 76 optimal weight:    9.9990
   overall best weight:    4.5186

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.052920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.039080 restraints weight = 196970.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.040927 restraints weight = 81679.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.042167 restraints weight = 46334.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.4333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  11229  Z= 0.203
  Angle     :  0.592   7.864  15227  Z= 0.315
  Chirality :  0.038   0.137   1784
  Planarity :  0.003   0.048   1887
  Dihedral  :  3.637  16.437   1474
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.64 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 22.72 %
    Favored  : 74.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    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:  0.73 (0.23), residues: 1375
  helix:  1.02 (0.17), residues: 901
  sheet: -0.13 (0.55), residues: 90
  loop : -0.45 (0.34), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 709 
 HIS   0.002   0.001   HIS A1185 
 PHE   0.016   0.001   PHE A 586 
 TYR   0.011   0.001   TYR A 101 
 ARG   0.003   0.000   ARG A1083 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04115 (  638)
  hydrogen bonds       : angle       4.92597 ( 1860)
  SS BOND              : bond        0.00210 (    1)
  SS BOND              : angle       0.42415 (    2)
  covalent geometry    : bond        0.00391 (11228)
  covalent geometry    : angle       0.59183 (15225)

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

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

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 143
  time to evaluate  : 1.616 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 GLU cc_start: 0.9759 (pt0) cc_final: 0.9532 (tm-30)
REVERT: A  107 TYR cc_start: 0.9664 (OUTLIER) cc_final: 0.9362 (m-10)
REVERT: A  387 LYS cc_start: 0.9252 (mtpt) cc_final: 0.8891 (mtpp)
REVERT: A  438 MET cc_start: 0.9396 (ppp) cc_final: 0.9156 (tmm)
REVERT: A  440 MET cc_start: 0.9177 (mmm) cc_final: 0.8830 (mmm)
REVERT: A  607 SER cc_start: 0.9545 (t) cc_final: 0.9307 (p)
REVERT: A 1460 LEU cc_start: 0.9747 (OUTLIER) cc_final: 0.9352 (tt)
  outliers start: 37
  outliers final: 31
  residues processed: 163
  average time/residue: 0.4000
  time to fit residues: 101.7397
Evaluate side-chains
  175 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 142
  time to evaluate  : 1.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 TRP
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  103 ASN
Chi-restraints excluded: chain A residue  107 TYR
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  110 THR
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  192 ASN
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  396 ILE
Chi-restraints excluded: chain A residue  432 MET
Chi-restraints excluded: chain A residue  458 GLU
Chi-restraints excluded: chain A residue  476 ILE
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  567 LEU
Chi-restraints excluded: chain A residue  596 LEU
Chi-restraints excluded: chain A residue  799 ILE
Chi-restraints excluded: chain A residue  971 LEU
Chi-restraints excluded: chain A residue 1032 LEU
Chi-restraints excluded: chain A residue 1056 LEU
Chi-restraints excluded: chain A residue 1065 LEU
Chi-restraints excluded: chain A residue 1134 TYR
Chi-restraints excluded: chain A residue 1209 ILE
Chi-restraints excluded: chain A residue 1327 MET
Chi-restraints excluded: chain A residue 1347 LEU
Chi-restraints excluded: chain A residue 1395 LEU
Chi-restraints excluded: chain A residue 1445 LEU
Chi-restraints excluded: chain A residue 1460 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 43 optimal weight:    0.7980
   chunk 95 optimal weight:    0.9980
   chunk 87 optimal weight:    3.9990
   chunk 36 optimal weight:   10.0000
   chunk 1 optimal weight:    2.9990
   chunk 39 optimal weight:    8.9990
   chunk 55 optimal weight:    6.9990
   chunk 120 optimal weight:    7.9990
   chunk 104 optimal weight:    7.9990
   chunk 3 optimal weight:    0.7980
   chunk 98 optimal weight:    6.9990
   overall best weight:    1.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 767 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.053746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.039687 restraints weight = 191493.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.041581 restraints weight = 78925.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.042843 restraints weight = 44652.446|
|-----------------------------------------------------------------------------|
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8279
moved from start:          0.4394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11229  Z= 0.122
  Angle     :  0.583   8.309  15227  Z= 0.295
  Chirality :  0.039   0.181   1784
  Planarity :  0.003   0.050   1887
  Dihedral  :  3.583  15.405   1474
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.05 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 22.48 %
    Favored  : 74.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    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:  1.06 (0.23), residues: 1375
  helix:  1.30 (0.17), residues: 899
  sheet: -0.12 (0.55), residues: 90
  loop : -0.34 (0.35), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 709 
 HIS   0.003   0.001   HIS A1162 
 PHE   0.010   0.001   PHE A 337 
 TYR   0.011   0.001   TYR A 319 
 ARG   0.003   0.000   ARG A1083 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04100 (  638)
  hydrogen bonds       : angle       4.61720 ( 1860)
  SS BOND              : bond        0.00046 (    1)
  SS BOND              : angle       0.11833 (    2)
  covalent geometry    : bond        0.00262 (11228)
  covalent geometry    : angle       0.58328 (15225)

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

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

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2750 Ramachandran restraints generated.
    1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 156
  time to evaluate  : 1.675 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 GLU cc_start: 0.9745 (pt0) cc_final: 0.9514 (tm-30)
REVERT: A  107 TYR cc_start: 0.9633 (OUTLIER) cc_final: 0.9326 (m-10)
REVERT: A  387 LYS cc_start: 0.9228 (mtpt) cc_final: 0.8864 (mtpp)
REVERT: A  438 MET cc_start: 0.9356 (ppp) cc_final: 0.9130 (tmm)
REVERT: A  440 MET cc_start: 0.9154 (mmm) cc_final: 0.8865 (mmm)
REVERT: A  502 MET cc_start: 0.9584 (ttp) cc_final: 0.8894 (ttp)
REVERT: A  607 SER cc_start: 0.9544 (t) cc_final: 0.9312 (p)
REVERT: A 1460 LEU cc_start: 0.9744 (OUTLIER) cc_final: 0.9353 (tt)
  outliers start: 39
  outliers final: 33
  residues processed: 175
  average time/residue: 0.4366
  time to fit residues: 120.7209
Evaluate side-chains
  185 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 150
  time to evaluate  : 1.764 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 TRP
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  103 ASN
Chi-restraints excluded: chain A residue  107 TYR
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  110 THR
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  192 ASN
Chi-restraints excluded: chain A residue  233 MET
Chi-restraints excluded: chain A residue  311 MET
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  432 MET
Chi-restraints excluded: chain A residue  458 GLU
Chi-restraints excluded: chain A residue  476 ILE
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  567 LEU
Chi-restraints excluded: chain A residue  596 LEU
Chi-restraints excluded: chain A residue  799 ILE
Chi-restraints excluded: chain A residue  971 LEU
Chi-restraints excluded: chain A residue 1032 LEU
Chi-restraints excluded: chain A residue 1056 LEU
Chi-restraints excluded: chain A residue 1065 LEU
Chi-restraints excluded: chain A residue 1134 TYR
Chi-restraints excluded: chain A residue 1209 ILE
Chi-restraints excluded: chain A residue 1226 MET
Chi-restraints excluded: chain A residue 1327 MET
Chi-restraints excluded: chain A residue 1347 LEU
Chi-restraints excluded: chain A residue 1395 LEU
Chi-restraints excluded: chain A residue 1445 LEU
Chi-restraints excluded: chain A residue 1452 LEU
Chi-restraints excluded: chain A residue 1460 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 114 optimal weight:    0.3980
   chunk 52 optimal weight:    5.9990
   chunk 50 optimal weight:    4.9990
   chunk 53 optimal weight:    6.9990
   chunk 89 optimal weight:   10.0000
   chunk 25 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9980
   chunk 49 optimal weight:    8.9990
   chunk 119 optimal weight:   10.0000
   chunk 18 optimal weight:    2.9990
   chunk 116 optimal weight:    0.9990
   overall best weight:    1.2584

-------------------------------------------------------------------------------
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 = 0.3404 r_free = 0.3404 target = 0.053990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.039906 restraints weight = 191586.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.041809 restraints weight = 79337.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.043075 restraints weight = 44999.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.3001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.4500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11229  Z= 0.117
  Angle     :  0.589   8.560  15227  Z= 0.296
  Chirality :  0.039   0.138   1784
  Planarity :  0.003   0.050   1887
  Dihedral  :  3.557  15.237   1474
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.35 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 23.70 %
    Favored  : 73.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    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:  1.16 (0.23), residues: 1375
  helix:  1.39 (0.17), residues: 895
  sheet: -0.09 (0.57), residues: 85
  loop : -0.32 (0.34), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 709 
 HIS   0.003   0.001   HIS A 439 
 PHE   0.013   0.001   PHE A1084 
 TYR   0.010   0.001   TYR A 319 
 ARG   0.002   0.000   ARG A 498 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04024 (  638)
  hydrogen bonds       : angle       4.54763 ( 1860)
  SS BOND              : bond        0.00045 (    1)
  SS BOND              : angle       0.08232 (    2)
  covalent geometry    : bond        0.00261 (11228)
  covalent geometry    : angle       0.58905 (15225)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6851.36 seconds
wall clock time: 119 minutes 41.99 seconds (7181.99 seconds total)