Starting phenix.real_space_refine
on Mon Aug 25 18:11:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hf0_34707/08_2025/8hf0_34707.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hf0_34707/08_2025/8hf0_34707.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.72
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hf0_34707/08_2025/8hf0_34707.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hf0_34707/08_2025/8hf0_34707.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hf0_34707/08_2025/8hf0_34707.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hf0_34707/08_2025/8hf0_34707.cif"
  }
  resolution = 3.72
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.007 sd=   0.046
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
     P      97      5.49       5
     S     153      5.16       5
     C   18503      2.51       5
     N    5028      2.21       5
     O    5729      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 29510
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 12634
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1561, 12634
          Classifications: {'peptide': 1561}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 65, 'TRANS': 1495}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 144
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 144
          Classifications: {'peptide': 16}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 15}
    Chain: "C"
      Number of atoms: 1027
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 1027
          Classifications: {'peptide': 126}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 122}
    Chain: "D"
      Number of atoms: 12634
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1561, 12634
          Classifications: {'peptide': 1561}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 65, 'TRANS': 1495}
          Chain breaks: 2
    Chain: "E"
      Number of atoms: 1010
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 1010
          Classifications: {'peptide': 124}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 120}
    Chain: "P"
      Number of atoms: 1003
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 1003
          Classifications: {'RNA': 47}
          Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 25, 'rna3p_pyr': 21}
          Link IDs: {'rna3p': 46}
    Chain: "N"
      Number of atoms: 1058
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 1058
          Classifications: {'RNA': 50}
          Modifications used: {'rna3p_pur': 23, 'rna3p_pyr': 27}
          Link IDs: {'rna3p': 49}
  Time building chain proxies: 5.59, per 1000 atoms: 0.19
  Number of scatterers: 29510
  At special positions: 0
  Unit cell: (160.056, 174.02, 183.688, 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     153     16.00
     P      97     15.00
     O    5729      8.00
     N    5028      7.00
     C   18503      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.60
  Conformation dependent library (CDL) restraints added in 977.8 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  6740 Ramachandran restraints generated.
    3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  6488

  Finding SS restraints...
    Secondary structure from input PDB file:
      157 helices and 26 sheets defined
      55.3% alpha, 11.7% beta
      42 base pairs and 73 stacking pairs defined.
    Time for finding SS restraints: 3.86
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 22
    Processing helix  chain 'A' and resid 31 through 45
      removed outlier: 4.082A  pdb=" N   THR A  35 " --> pdb=" O   GLY A  31 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   ALA A  38 " --> pdb=" O   LYS A  34 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   PHE A  45 " --> pdb=" O   VAL A  41 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 50
      removed outlier: 3.588A  pdb=" N   PHE A  49 " --> pdb=" O   SER A  46 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   ASP A  50 " --> pdb=" O   GLN A  47 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 46 through 50'
    Processing helix  chain 'A' and resid 66 through 81
    Processing helix  chain 'A' and resid 89 through 93
    Processing helix  chain 'A' and resid 98 through 109
    Processing helix  chain 'A' and resid 116 through 125
    Processing helix  chain 'A' and resid 129 through 131
      No H-bonds generated for 'chain 'A' and resid 129 through 131'
    Processing helix  chain 'A' and resid 140 through 144
    Processing helix  chain 'A' and resid 148 through 156
    Processing helix  chain 'A' and resid 157 through 159
      No H-bonds generated for 'chain 'A' and resid 157 through 159'
    Processing helix  chain 'A' and resid 161 through 165
    Processing helix  chain 'A' and resid 183 through 195
      removed outlier: 3.592A  pdb=" N   LYS A 187 " --> pdb=" O   ASN A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 213
    Processing helix  chain 'A' and resid 232 through 251
      removed outlier: 3.609A  pdb=" N   ARG A 236 " --> pdb=" O   LEU A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 292
      removed outlier: 3.644A  pdb=" N   VAL A 277 " --> pdb=" O   LYS A 273 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   GLY A 292 " --> pdb=" O   MET A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 314
    Processing helix  chain 'A' and resid 316 through 345
      removed outlier: 3.642A  pdb=" N   MET A 344 " --> pdb=" O   LYS A 340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 350 through 362
    Processing helix  chain 'A' and resid 364 through 379
    Processing helix  chain 'A' and resid 394 through 410
      removed outlier: 3.606A  pdb=" N   CYS A 398 " --> pdb=" O   ARG A 394 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   LYS A 399 " --> pdb=" O   ARG A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 445 through 452
    Processing helix  chain 'A' and resid 484 through 495
      removed outlier: 3.858A  pdb=" N   ALA A 495 " --> pdb=" O   SER A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 510 through 535
      removed outlier: 3.633A  pdb=" N   THR A 514 " --> pdb=" O   GLU A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 543 through 550
    Processing helix  chain 'A' and resid 567 through 569
      No H-bonds generated for 'chain 'A' and resid 567 through 569'
    Processing helix  chain 'A' and resid 570 through 582
    Processing helix  chain 'A' and resid 598 through 607
    Processing helix  chain 'A' and resid 608 through 611
    Processing helix  chain 'A' and resid 637 through 656
    Processing helix  chain 'A' and resid 667 through 680
      removed outlier: 4.303A  pdb=" N   ASP A 677 " --> pdb=" O   ALA A 673 " (cutoff:3.500A)
      removed outlier: 4.773A  pdb=" N   VAL A 678 " --> pdb=" O   SER A 674 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 681 through 687
      removed outlier: 3.661A  pdb=" N   LYS A 685 " --> pdb=" O   HIS A 682 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 710 through 714
    Processing helix  chain 'A' and resid 741 through 749
      removed outlier: 3.802A  pdb=" N   ASN A 747 " --> pdb=" O   HIS A 743 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 792 through 810
      removed outlier: 3.604A  pdb=" N   LEU A 796 " --> pdb=" O   ASN A 792 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   PHE A 807 " --> pdb=" O   HIS A 803 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 845 through 852
    Processing helix  chain 'A' and resid 862 through 869
    Processing helix  chain 'A' and resid 873 through 878
    Processing helix  chain 'A' and resid 916 through 930
      removed outlier: 6.987A  pdb=" N   ASN A 927 " --> pdb=" O   SER A 923 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   ARG A 928 " --> pdb=" O   LYS A 924 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 960 through 967
    Processing helix  chain 'A' and resid 972 through 974
      No H-bonds generated for 'chain 'A' and resid 972 through 974'
    Processing helix  chain 'A' and resid 983 through 990
      removed outlier: 4.574A  pdb=" N   LYS A 988 " --> pdb=" O   ASP A 984 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 991 through 1016
      removed outlier: 3.734A  pdb=" N   HIS A1004 " --> pdb=" O   TYR A1000 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1174 through 1182
    Processing helix  chain 'A' and resid 1190 through 1199
    Processing helix  chain 'A' and resid 1209 through 1232
      removed outlier: 3.764A  pdb=" N   LEU A1215 " --> pdb=" O   ARG A1211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1236 through 1248
    Processing helix  chain 'A' and resid 1249 through 1259
      removed outlier: 3.926A  pdb=" N   ASP A1259 " --> pdb=" O   PHE A1255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1260 through 1266
      Proline residue:  A1263  - end of helix
    Processing helix  chain 'A' and resid 1272 through 1277
      removed outlier: 3.725A  pdb=" N   TRP A1277 " --> pdb=" O   PRO A1273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1285 through 1295
    Processing helix  chain 'A' and resid 1295 through 1300
    Processing helix  chain 'A' and resid 1303 through 1310
      removed outlier: 3.581A  pdb=" N   LEU A1307 " --> pdb=" O   GLY A1303 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   LEU A1310 " --> pdb=" O   ASN A1306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1313 through 1319
    Processing helix  chain 'A' and resid 1324 through 1339
    Processing helix  chain 'A' and resid 1348 through 1357
      removed outlier: 6.030A  pdb=" N   PHE A1354 " --> pdb=" O   SER A1350 " (cutoff:3.500A)
      removed outlier: 5.500A  pdb=" N   CYS A1355 " --> pdb=" O   GLU A1351 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   VAL A1356 " --> pdb=" O   VAL A1352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1363 through 1387
      removed outlier: 3.577A  pdb=" N   LEU A1370 " --> pdb=" O   ILE A1366 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ASN A1380 " --> pdb=" O   VAL A1376 " (cutoff:3.500A)
      removed outlier: 8.354A  pdb=" N   LEU A1383 " --> pdb=" O   LYS A1379 " (cutoff:3.500A)
      removed outlier: 9.268A  pdb=" N   GLN A1384 " --> pdb=" O   ASN A1380 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   HIS A1385 " --> pdb=" O   TYR A1381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1387 through 1393
      removed outlier: 4.136A  pdb=" N   GLU A1391 " --> pdb=" O   PHE A1387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1403 through 1407
    Processing helix  chain 'A' and resid 1422 through 1430
      removed outlier: 3.778A  pdb=" N   ILE A1426 " --> pdb=" O   ASN A1422 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   PHE A1429 " --> pdb=" O   GLU A1425 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1432 through 1441
    Processing helix  chain 'A' and resid 1447 through 1455
    Processing helix  chain 'A' and resid 1468 through 1491
      removed outlier: 3.572A  pdb=" N   ILE A1474 " --> pdb=" O   GLU A1470 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ALA A1477 " --> pdb=" O   PHE A1473 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1495 through 1508
    Processing helix  chain 'A' and resid 1508 through 1519
    Processing helix  chain 'A' and resid 1520 through 1525
      removed outlier: 3.860A  pdb=" N   PHE A1523 " --> pdb=" O   ARG A1520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1529 through 1547
    Processing helix  chain 'A' and resid 1609 through 1628
      removed outlier: 4.219A  pdb=" N   GLY A1613 " --> pdb=" O   PRO A1609 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1629 through 1651
      Proline residue:  A1643  - end of helix
      removed outlier: 4.009A  pdb=" N   ARG A1650 " --> pdb=" O   GLN A1646 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1655 through 1662
    Processing helix  chain 'A' and resid 1701 through 1721
    Processing helix  chain 'C' and resid 189 through 210
      removed outlier: 4.057A  pdb=" N   LEU C 193 " --> pdb=" O   SER C 189 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   GLU C 194 " --> pdb=" O   MET C 190 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   GLU C 209 " --> pdb=" O   TRP C 205 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 221 through 230
      removed outlier: 4.591A  pdb=" N   PHE C 227 " --> pdb=" O   HIS C 224 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   PHE C 230 " --> pdb=" O   PHE C 227 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 231 through 243
    Processing helix  chain 'C' and resid 249 through 260
      removed outlier: 3.512A  pdb=" N   LYS C 253 " --> pdb=" O   SER C 249 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 297 through 311
      removed outlier: 3.693A  pdb=" N   TYR C 305 " --> pdb=" O   HIS C 301 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 10 through 20
      removed outlier: 3.890A  pdb=" N   ARG D  14 " --> pdb=" O   GLY D  10 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 32 through 45
    Processing helix  chain 'D' and resid 46 through 50
      removed outlier: 3.583A  pdb=" N   PHE D  49 " --> pdb=" O   SER D  46 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   ASP D  50 " --> pdb=" O   GLN D  47 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 46 through 50'
    Processing helix  chain 'D' and resid 52 through 56
    Processing helix  chain 'D' and resid 66 through 81
    Processing helix  chain 'D' and resid 98 through 109
    Processing helix  chain 'D' and resid 116 through 125
    Processing helix  chain 'D' and resid 129 through 131
      No H-bonds generated for 'chain 'D' and resid 129 through 131'
    Processing helix  chain 'D' and resid 140 through 144
      removed outlier: 3.530A  pdb=" N   HIS D 143 " --> pdb=" O   GLU D 140 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 148 through 160
      removed outlier: 3.687A  pdb=" N   THR D 158 " --> pdb=" O   MET D 154 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   ILE D 159 " --> pdb=" O   ARG D 155 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   ALA D 160 " --> pdb=" O   LEU D 156 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 161 through 165
      removed outlier: 3.522A  pdb=" N   LEU D 165 " --> pdb=" O   GLN D 162 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 183 through 195
      removed outlier: 3.871A  pdb=" N   LYS D 187 " --> pdb=" O   ASN D 183 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 204 through 212
      removed outlier: 3.975A  pdb=" N   MET D 212 " --> pdb=" O   MET D 208 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 232 through 250
      removed outlier: 4.301A  pdb=" N   ARG D 236 " --> pdb=" O   LEU D 232 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 271 through 292
    Processing helix  chain 'D' and resid 292 through 314
      removed outlier: 3.946A  pdb=" N   ILE D 301 " --> pdb=" O   SER D 297 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   SER D 302 " --> pdb=" O   ILE D 298 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 316 through 343
    Processing helix  chain 'D' and resid 344 through 348
      removed outlier: 3.635A  pdb=" N   ASP D 347 " --> pdb=" O   MET D 344 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 350 through 362
      removed outlier: 3.916A  pdb=" N   ILE D 359 " --> pdb=" O   THR D 355 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 364 through 378
    Processing helix  chain 'D' and resid 382 through 386
      removed outlier: 3.759A  pdb=" N   ILE D 386 " --> pdb=" O   PRO D 383 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 394 through 412
      removed outlier: 3.517A  pdb=" N   CYS D 398 " --> pdb=" O   ARG D 394 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   LYS D 399 " --> pdb=" O   ARG D 395 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 414 through 419
      removed outlier: 4.332A  pdb=" N   VAL D 418 " --> pdb=" O   GLU D 414 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 445 through 452
    Processing helix  chain 'D' and resid 484 through 494
    Processing helix  chain 'D' and resid 510 through 535
    Processing helix  chain 'D' and resid 543 through 552
    Processing helix  chain 'D' and resid 567 through 569
      No H-bonds generated for 'chain 'D' and resid 567 through 569'
    Processing helix  chain 'D' and resid 570 through 582
      removed outlier: 3.636A  pdb=" N   ILE D 582 " --> pdb=" O   TYR D 578 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 598 through 607
    Processing helix  chain 'D' and resid 608 through 611
    Processing helix  chain 'D' and resid 637 through 656
    Processing helix  chain 'D' and resid 667 through 680
      removed outlier: 3.906A  pdb=" N   ILE D 675 " --> pdb=" O   ARG D 671 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   ASP D 677 " --> pdb=" O   ALA D 673 " (cutoff:3.500A)
      removed outlier: 5.406A  pdb=" N   VAL D 678 " --> pdb=" O   SER D 674 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 681 through 687
      removed outlier: 3.628A  pdb=" N   LYS D 685 " --> pdb=" O   HIS D 682 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 693 through 697
    Processing helix  chain 'D' and resid 741 through 748
      removed outlier: 3.856A  pdb=" N   LEU D 746 " --> pdb=" O   GLU D 742 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 792 through 810
    Processing helix  chain 'D' and resid 845 through 852
    Processing helix  chain 'D' and resid 862 through 866
    Processing helix  chain 'D' and resid 873 through 878
      removed outlier: 3.551A  pdb=" N   PHE D 877 " --> pdb=" O   ARG D 873 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 918 through 930
      removed outlier: 7.520A  pdb=" N   ASN D 927 " --> pdb=" O   SER D 923 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   ARG D 928 " --> pdb=" O   LYS D 924 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 960 through 965
    Processing helix  chain 'D' and resid 972 through 976
    Processing helix  chain 'D' and resid 982 through 1017
      Proline residue:  D 993  - end of helix
    Processing helix  chain 'D' and resid 1018 through 1025
      Proline residue:  D1022  - end of helix
    Processing helix  chain 'D' and resid 1174 through 1182
    Processing helix  chain 'D' and resid 1183 through 1186
    Processing helix  chain 'D' and resid 1190 through 1199
    Processing helix  chain 'D' and resid 1209 through 1232
      removed outlier: 4.071A  pdb=" N   LEU D1215 " --> pdb=" O   ARG D1211 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1236 through 1248
    Processing helix  chain 'D' and resid 1249 through 1261
      removed outlier: 3.766A  pdb=" N   ASP D1259 " --> pdb=" O   PHE D1255 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1262 through 1266
      removed outlier: 3.587A  pdb=" N   LEU D1266 " --> pdb=" O   PRO D1263 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1272 through 1277
      removed outlier: 3.806A  pdb=" N   TRP D1277 " --> pdb=" O   PRO D1273 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1285 through 1295
    Processing helix  chain 'D' and resid 1297 through 1302
      removed outlier: 3.506A  pdb=" N   LYS D1300 " --> pdb=" O   GLU D1297 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ILE D1301 " --> pdb=" O   PHE D1298 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ILE D1302 " --> pdb=" O   ALA D1299 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 1297 through 1302'
    Processing helix  chain 'D' and resid 1303 through 1308
    Processing helix  chain 'D' and resid 1313 through 1319
    Processing helix  chain 'D' and resid 1324 through 1337
    Processing helix  chain 'D' and resid 1338 through 1341
      removed outlier: 3.538A  pdb=" N   SER D1341 " --> pdb=" O   ASN D1338 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 1338 through 1341'
    Processing helix  chain 'D' and resid 1348 through 1351
      removed outlier: 3.598A  pdb=" N   GLU D1351 " --> pdb=" O   PHE D1348 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 1348 through 1351'
    Processing helix  chain 'D' and resid 1352 through 1357
      removed outlier: 3.695A  pdb=" N   VAL D1356 " --> pdb=" O   VAL D1352 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1362 through 1387
      removed outlier: 8.005A  pdb=" N   LEU D1383 " --> pdb=" O   LYS D1379 " (cutoff:3.500A)
      removed outlier: 9.279A  pdb=" N   GLN D1384 " --> pdb=" O   ASN D1380 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   HIS D1385 " --> pdb=" O   TYR D1381 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1387 through 1393
      removed outlier: 4.117A  pdb=" N   GLU D1391 " --> pdb=" O   PHE D1387 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1403 through 1407
    Processing helix  chain 'D' and resid 1422 through 1428
    Processing helix  chain 'D' and resid 1432 through 1441
    Processing helix  chain 'D' and resid 1446 through 1455
      removed outlier: 4.392A  pdb=" N   LEU D1450 " --> pdb=" O   ASP D1446 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1468 through 1491
      removed outlier: 3.805A  pdb=" N   ILE D1474 " --> pdb=" O   GLU D1470 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   ALA D1477 " --> pdb=" O   PHE D1473 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1495 through 1508
    Processing helix  chain 'D' and resid 1508 through 1519
    Processing helix  chain 'D' and resid 1521 through 1525
    Processing helix  chain 'D' and resid 1529 through 1546
    Processing helix  chain 'D' and resid 1609 through 1628
      removed outlier: 4.340A  pdb=" N   GLY D1613 " --> pdb=" O   PRO D1609 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LEU D1616 " --> pdb=" O   LEU D1612 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1629 through 1651
      Proline residue:  D1643  - end of helix
    Processing helix  chain 'D' and resid 1655 through 1663
    Processing helix  chain 'D' and resid 1701 through 1721
    Processing helix  chain 'E' and resid 189 through 210
      removed outlier: 3.913A  pdb=" N   ARG E 197 " --> pdb=" O   LEU E 193 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 222 through 230
      removed outlier: 4.237A  pdb=" N   PHE E 227 " --> pdb=" O   HIS E 224 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   PHE E 230 " --> pdb=" O   PHE E 227 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 231 through 243
      removed outlier: 3.997A  pdb=" N   GLU E 237 " --> pdb=" O   THR E 233 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 249 through 261
    Processing helix  chain 'E' and resid 295 through 310
      removed outlier: 4.620A  pdb=" N   TYR E 299 " --> pdb=" O   GLU E 295 " (cutoff:3.500A)
      removed outlier: 5.259A  pdb=" N   ASP E 300 " --> pdb=" O   THR E 296 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 88
      removed outlier: 3.599A  pdb=" N   THR A 115 " --> pdb=" O   TYR A  88 " (cutoff:3.500A)
      removed outlier: 7.139A  pdb=" N   ARG A  59 " --> pdb=" O   SER A 134 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   VAL A 136 " --> pdb=" O   ARG A  59 " (cutoff:3.500A)
      removed outlier: 7.150A  pdb=" N   LEU A  61 " --> pdb=" O   VAL A 136 " (cutoff:3.500A)
      removed outlier: 6.070A  pdb=" N   ILE A 138 " --> pdb=" O   LEU A  61 " (cutoff:3.500A)
      removed outlier: 7.538A  pdb=" N   MET A  63 " --> pdb=" O   ILE A 138 " (cutoff:3.500A)
      removed outlier: 7.381A  pdb=" N   GLY A  24 " --> pdb=" O   GLY A 170 " (cutoff:3.500A)
      removed outlier: 8.000A  pdb=" N   THR A 172 " --> pdb=" O   GLY A  24 " (cutoff:3.500A)
      removed outlier: 6.190A  pdb=" N   VAL A  26 " --> pdb=" O   THR A 172 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   ILE A  25 " --> pdb=" O   ILE A 200 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 457 through 460
      removed outlier: 6.259A  pdb=" N   LEU A 389 " --> pdb=" O   PHE A 477 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 260 through 261
      removed outlier: 4.540A  pdb=" N   ARG A 260 " --> pdb=" O   ARG A 269 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 558 through 559
      removed outlier: 3.568A  pdb=" N   PHE A 558 " --> pdb=" O   LEU A 566 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 593 through 596
    Processing sheet with id=AA6, first strand: chain 'A' and resid 702 through 706
    Processing sheet with id=AA7, first strand: chain 'A' and resid 768 through 771
    Processing sheet with id=AA8, first strand: chain 'A' and resid 768 through 771
      removed outlier: 4.793A  pdb=" N   TYR A 754 " --> pdb=" O   ILE A 729 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ASN A 753 " --> pdb=" O   LEU A 834 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 819 through 820
    Processing sheet with id=AB1, first strand: chain 'A' and resid 969 through 971
      removed outlier: 4.082A  pdb=" N   VAL A 969 " --> pdb=" O   VAL A 942 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   LYS A 897 " --> pdb=" O   GLU A 941 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   ARG A 943 " --> pdb=" O   VAL A 895 " (cutoff:3.500A)
      removed outlier: 4.960A  pdb=" N   VAL A 895 " --> pdb=" O   ARG A 943 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   VAL A 895 " --> pdb=" O   LYS A 880 " (cutoff:3.500A)
      removed outlier: 4.840A  pdb=" N   LYS A 880 " --> pdb=" O   VAL A 895 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   ILE A 881 " --> pdb=" O   PHE A 979 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 1554 through 1558
      removed outlier: 6.639A  pdb=" N   MET A1602 " --> pdb=" O   LEU A1557 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   SER A1603 " --> pdb=" O   PHE A1698 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 1554 through 1558
      removed outlier: 6.639A  pdb=" N   MET A1602 " --> pdb=" O   LEU A1557 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   SER A1603 " --> pdb=" O   PHE A1698 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 268 through 270
      removed outlier: 4.247A  pdb=" N   LEU C 278 " --> pdb=" O   VAL C 270 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 86 through 88
      removed outlier: 3.549A  pdb=" N   VAL D 113 " --> pdb=" O   GLY D  86 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR D 115 " --> pdb=" O   TYR D  88 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   ALA D  60 " --> pdb=" O   LEU D 112 " (cutoff:3.500A)
      removed outlier: 8.014A  pdb=" N   GLY D 114 " --> pdb=" O   ALA D  60 " (cutoff:3.500A)
      removed outlier: 6.031A  pdb=" N   PHE D  62 " --> pdb=" O   GLY D 114 " (cutoff:3.500A)
      removed outlier: 5.672A  pdb=" N   ARG D  59 " --> pdb=" O   LEU D 133 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   VAL D 135 " --> pdb=" O   ARG D  59 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   LEU D  61 " --> pdb=" O   VAL D 135 " (cutoff:3.500A)
      removed outlier: 6.874A  pdb=" N   SER D 134 " --> pdb=" O   ARG D 167 " (cutoff:3.500A)
      removed outlier: 8.215A  pdb=" N   VAL D 169 " --> pdb=" O   SER D 134 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   VAL D 136 " --> pdb=" O   VAL D 169 " (cutoff:3.500A)
      removed outlier: 7.489A  pdb=" N   LEU D 171 " --> pdb=" O   VAL D 136 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   ILE D 138 " --> pdb=" O   LEU D 171 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   THR D 172 " --> pdb=" O   VAL D  26 " (cutoff:3.500A)
      removed outlier: 5.831A  pdb=" N   ILE D  25 " --> pdb=" O   ILE D 200 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 219 through 225
      removed outlier: 6.595A  pdb=" N   VAL D 476 " --> pdb=" O   VAL D 503 " (cutoff:3.500A)
      removed outlier: 8.031A  pdb=" N   PHE D 505 " --> pdb=" O   VAL D 476 " (cutoff:3.500A)
      removed outlier: 7.450A  pdb=" N   ILE D 478 " --> pdb=" O   PHE D 505 " (cutoff:3.500A)
      removed outlier: 9.220A  pdb=" N   ALA D 507 " --> pdb=" O   ILE D 478 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   CYS D 388 " --> pdb=" O   MET D 458 " (cutoff:3.500A)
      removed outlier: 7.892A  pdb=" N   CYS D 460 " --> pdb=" O   CYS D 388 " (cutoff:3.500A)
      removed outlier: 6.024A  pdb=" N   VAL D 390 " --> pdb=" O   CYS D 460 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   GLN D 422 " --> pdb=" O   ILE D 459 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 260 through 261
      removed outlier: 4.362A  pdb=" N   ARG D 260 " --> pdb=" O   ARG D 269 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 558 through 559
    Processing sheet with id=AB9, first strand: chain 'D' and resid 593 through 596
    Processing sheet with id=AC1, first strand: chain 'D' and resid 703 through 706
    Processing sheet with id=AC2, first strand: chain 'D' and resid 768 through 771
    Processing sheet with id=AC3, first strand: chain 'D' and resid 768 through 771
      removed outlier: 3.585A  pdb=" N   ILE D 729 " --> pdb=" O   TYR D 754 " (cutoff:3.500A)
      removed outlier: 5.806A  pdb=" N   TYR D 754 " --> pdb=" O   ILE D 729 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LEU D 830 " --> pdb=" O   LEU D 757 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'D' and resid 819 through 820
    Processing sheet with id=AC5, first strand: chain 'D' and resid 970 through 971
      removed outlier: 3.794A  pdb=" N   LEU D 971 " --> pdb=" O   ILE D 940 " (cutoff:3.500A)
      removed outlier: 6.059A  pdb=" N   ARG D 943 " --> pdb=" O   VAL D 895 " (cutoff:3.500A)
      removed outlier: 4.845A  pdb=" N   VAL D 895 " --> pdb=" O   ARG D 943 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'D' and resid 1554 through 1558
      removed outlier: 7.347A  pdb=" N   MET D1602 " --> pdb=" O   LEU D1557 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   SER D1603 " --> pdb=" O   PHE D1698 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'D' and resid 1554 through 1558
      removed outlier: 7.347A  pdb=" N   MET D1602 " --> pdb=" O   LEU D1557 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   SER D1603 " --> pdb=" O   PHE D1698 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'E' and resid 267 through 270
      removed outlier: 4.311A  pdb=" N   LEU E 278 " --> pdb=" O   VAL E 270 " (cutoff:3.500A)

    1392 hydrogen bonds defined for protein.
    3924 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      102 hydrogen bonds
      196 hydrogen bond angles
      0 basepair planarities
      42 basepair parallelities
      73 stacking parallelities
  Total time for adding SS restraints: 7.29

  Time building geometry restraints manager: 3.18 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 9107
        1.34 -     1.46: 5382
        1.46 -     1.58: 15411
        1.58 -     1.70: 192
        1.70 -     1.82: 242
  Bond restraints: 30334
  Sorted by residual:
  bond pdb=" CG1 ILE D1258 "
       pdb=" CD1 ILE D1258 "
    ideal  model  delta    sigma   weight residual
    1.513  1.439  0.074 3.90e-02 6.57e+02 3.56e+00
  bond pdb=" CG  LEU C 193 "
       pdb=" CD1 LEU C 193 "
    ideal  model  delta    sigma   weight residual
    1.521  1.462  0.059 3.30e-02 9.18e+02 3.18e+00
  bond pdb=" CB  GLU A1371 "
       pdb=" CG  GLU A1371 "
    ideal  model  delta    sigma   weight residual
    1.520  1.480  0.040 3.00e-02 1.11e+03 1.77e+00
  bond pdb=" C   ILE D1262 "
       pdb=" N   PRO D1263 "
    ideal  model  delta    sigma   weight residual
    1.334  1.361 -0.027 2.34e-02 1.83e+03 1.33e+00
  bond pdb=" CA  MET A 967 "
       pdb=" CB  MET A 967 "
    ideal  model  delta    sigma   weight residual
    1.523  1.537 -0.014 1.21e-02 6.83e+03 1.26e+00
  ... (remaining 30329 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.53: 41117
        2.53 -     5.07: 335
        5.07 -     7.60: 31
        7.60 -    10.14: 3
       10.14 -    12.67: 2
  Bond angle restraints: 41488
  Sorted by residual:
  angle pdb=" N   GLY D 957 "
        pdb=" CA  GLY D 957 "
        pdb=" C   GLY D 957 "
      ideal   model   delta    sigma   weight residual
     111.35  116.42   -5.07 1.20e+00 6.94e-01 1.79e+01
  angle pdb=" CB  MET A 620 "
        pdb=" CG  MET A 620 "
        pdb=" SD  MET A 620 "
      ideal   model   delta    sigma   weight residual
     112.70  125.37  -12.67 3.00e+00 1.11e-01 1.78e+01
  angle pdb=" CG  ARG B 346 "
        pdb=" CD  ARG B 346 "
        pdb=" NE  ARG B 346 "
      ideal   model   delta    sigma   weight residual
     112.00  119.73   -7.73 2.20e+00 2.07e-01 1.24e+01
  angle pdb=" CA  ALA C 286 "
        pdb=" C   ALA C 286 "
        pdb=" N   PHE C 287 "
      ideal   model   delta    sigma   weight residual
     118.27  113.51    4.76 1.59e+00 3.96e-01 8.98e+00
  angle pdb=" N   ILE D 582 "
        pdb=" CA  ILE D 582 "
        pdb=" C   ILE D 582 "
      ideal   model   delta    sigma   weight residual
     108.88  115.26   -6.38 2.16e+00 2.14e-01 8.72e+00
  ... (remaining 41483 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.45: 17791
       31.45 -    62.90: 596
       62.90 -    94.34: 146
       94.34 -   125.79: 1
      125.79 -   157.24: 1
  Dihedral angle restraints: 18535
    sinusoidal: 8537
      harmonic: 9998
  Sorted by residual:
  dihedral pdb=" CA  CYS C 285 "
           pdb=" C   CYS C 285 "
           pdb=" N   ALA C 286 "
           pdb=" CA  ALA C 286 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.67   25.33     0      5.00e+00 4.00e-02 2.57e+01
  dihedral pdb=" CA  MET D 101 "
           pdb=" C   MET D 101 "
           pdb=" N   TRP D 102 "
           pdb=" CA  TRP D 102 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.01   24.99     0      5.00e+00 4.00e-02 2.50e+01
  dihedral pdb=" CA  ARG A 427 "
           pdb=" C   ARG A 427 "
           pdb=" N   ASN A 428 "
           pdb=" CA  ASN A 428 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.99  -20.01     0      5.00e+00 4.00e-02 1.60e+01
  ... (remaining 18532 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 3260
       0.035 -    0.070: 1026
       0.070 -    0.105: 342
       0.105 -    0.140: 97
       0.140 -    0.175: 8
  Chirality restraints: 4733
  Sorted by residual:
  chirality pdb=" C3'   C N  27 "
            pdb=" C4'   C N  27 "
            pdb=" O3'   C N  27 "
            pdb=" C2'   C N  27 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.30   -0.18 2.00e-01 2.50e+01 7.68e-01
  chirality pdb=" CA  ILE A1654 "
            pdb=" N   ILE A1654 "
            pdb=" C   ILE A1654 "
            pdb=" CB  ILE A1654 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 6.93e-01
  chirality pdb=" CG  LEU D 992 "
            pdb=" CB  LEU D 992 "
            pdb=" CD1 LEU D 992 "
            pdb=" CD2 LEU D 992 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.56e-01
  ... (remaining 4730 not shown)

  Planarity restraints: 4953
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 370 "    0.015 2.00e-02 2.50e+03   1.65e-02 4.76e+00
        pdb=" CG  PHE A 370 "   -0.038 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 370 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 370 "    0.013 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 370 "    0.006 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 370 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 370 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR D 903 "    0.035 5.00e-02 4.00e+02   5.34e-02 4.56e+00
        pdb=" N   PRO D 904 "   -0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO D 904 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO D 904 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET D 101 "    0.009 2.00e-02 2.50e+03   1.86e-02 3.46e+00
        pdb=" C   MET D 101 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   MET D 101 "    0.012 2.00e-02 2.50e+03
        pdb=" N   TRP D 102 "    0.011 2.00e-02 2.50e+03
  ... (remaining 4950 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 895
        2.71 -     3.25: 31454
        3.25 -     3.80: 49744
        3.80 -     4.35: 63108
        4.35 -     4.90: 99879
  Nonbonded interactions: 245080
  Sorted by model distance:
  nonbonded pdb=" OG  SER D 264 "
            pdb=" OE1 GLN D 266 "
     model   vdw
     2.157 3.040
  nonbonded pdb=" OG  SER E 244 "
            pdb=" OE1 GLU E 246 "
     model   vdw
     2.165 3.040
  nonbonded pdb=" OG1 THR D 182 "
            pdb=" OP1   A N  18 "
     model   vdw
     2.175 3.040
  nonbonded pdb=" OD1 ASP A 944 "
            pdb=" N   LEU A 945 "
     model   vdw
     2.188 3.120
  nonbonded pdb=" O   LEU A 341 "
            pdb=" OG1 THR A 345 "
     model   vdw
     2.195 3.040
  ... (remaining 245075 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'D'
}
ncs_group {
  reference = (chain 'C' and resid 188 through 311)
  selection = chain 'E'
}
ncs_group {
  reference = (chain 'N' and resid 3 through 47)
  selection = (chain 'P' and resid 3 through 47)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.990
  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:             0.020
  Extract box with map and model:          0.450
  Check model and map are aligned:         0.090
  Set scattering table:                    0.080
  Process input model:                     28.460
  Find NCS groups from input model:        0.370
  Set up NCS constraints:                  0.060
  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:1.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
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   0.074  30334  Z= 0.125
  Angle     :  0.574  12.674  41488  Z= 0.300
  Chirality :  0.040   0.175   4733
  Planarity :  0.004   0.053   4953
  Dihedral  : 15.853 157.241  12047
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  3.41 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.32 (0.15), residues: 3370
  helix:  0.87 (0.13), residues: 1591
  sheet: -0.57 (0.26), residues: 363
  loop : -0.18 (0.17), residues: 1416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 604 
 TYR   0.014   0.001   TYR D1328 
 PHE   0.038   0.001   PHE A 370 
 TRP   0.022   0.002   TRP D 814 
 HIS   0.014   0.001   HIS C 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (30334)
  covalent geometry    : angle       0.57397 (41488)
  hydrogen bonds       : bond        0.17367 ( 1454)
  hydrogen bonds       : angle       6.39253 ( 4120)

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

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

  6740 Ramachandran restraints generated.
    3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6740 Ramachandran restraints generated.
    3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 299
  time to evaluate  : 0.953 
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: A  176 ILE cc_start: 0.7060 (mm) cc_final: 0.6686 (mm)
REVERT: A  317 LEU cc_start: 0.8314 (tp) cc_final: 0.7983 (tp)
REVERT: A  494 ARG cc_start: 0.6537 (mmp-170) cc_final: 0.6140 (mmm160)
REVERT: A  531 TYR cc_start: 0.8574 (t80) cc_final: 0.8354 (t80)
REVERT: C  223 ARG cc_start: 0.7793 (ptt-90) cc_final: 0.7510 (ptt-90)
REVERT: D  714 TYR cc_start: 0.8793 (t80) cc_final: 0.8513 (t80)
REVERT: D  794 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8275 (pp20)
REVERT: D 1209 MET cc_start: 0.7871 (mtm) cc_final: 0.7411 (mtm)
REVERT: D 1333 GLU cc_start: 0.9264 (mt-10) cc_final: 0.8916 (pt0)
  outliers start: 0
  outliers final: 0
  residues processed: 299
  average time/residue: 0.1663
  time to fit residues: 82.1973
Evaluate side-chains
  223 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 223
  time to evaluate  : 0.803 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 346
   random chunks:
   chunk 197 optimal weight:    0.8980
   chunk 215 optimal weight:    7.9990
   chunk 20 optimal weight:    5.9990
   chunk 132 optimal weight:    6.9990
   chunk 261 optimal weight:    5.9990
   chunk 248 optimal weight:    8.9990
   chunk 207 optimal weight:    1.9990
   chunk 155 optimal weight:    9.9990
   chunk 244 optimal weight:   30.0000
   chunk 183 optimal weight:    3.9990
   chunk 298 optimal weight:    1.9990
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 301 HIS
D 253 ASN
D 747 ASN
** D 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D1305 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.085906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.063081 restraints weight = 127740.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.065084 restraints weight = 71213.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.065414 restraints weight = 45222.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.065786 restraints weight = 38076.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.065807 restraints weight = 34531.355|
|-----------------------------------------------------------------------------|
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.1221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.079  30334  Z= 0.175
  Angle     :  0.624  10.595  41488  Z= 0.323
  Chirality :  0.042   0.302   4733
  Planarity :  0.004   0.051   4953
  Dihedral  : 14.212 160.270   5192
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  3.59 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  :  7.04 %
    Favored  : 92.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.19 (0.14), residues: 3370
  helix:  0.84 (0.13), residues: 1609
  sheet: -0.75 (0.25), residues: 391
  loop : -0.31 (0.17), residues: 1370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 719 
 TYR   0.018   0.002   TYR A1468 
 PHE   0.019   0.002   PHE A1001 
 TRP   0.020   0.002   TRP D 814 
 HIS   0.007   0.001   HIS D1185 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 (30334)
  covalent geometry    : angle       0.62378 (41488)
  hydrogen bonds       : bond        0.04978 ( 1454)
  hydrogen bonds       : angle       4.94045 ( 4120)

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

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

  6740 Ramachandran restraints generated.
    3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6740 Ramachandran restraints generated.
    3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 237
  time to evaluate  : 1.177 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  236 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8287 (mpp80)
REVERT: A  344 MET cc_start: 0.8147 (mmm) cc_final: 0.7776 (mmm)
REVERT: A  531 TYR cc_start: 0.8724 (t80) cc_final: 0.8496 (t80)
REVERT: A  589 PHE cc_start: 0.7693 (t80) cc_final: 0.7462 (t80)
REVERT: A  620 MET cc_start: 0.8891 (mmm) cc_final: 0.8169 (mmm)
REVERT: A  939 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.6990 (mmp)
REVERT: A 1343 TYR cc_start: 0.8098 (m-80) cc_final: 0.7838 (m-80)
REVERT: A 1417 MET cc_start: 0.1541 (tpt) cc_final: 0.1285 (tpt)
REVERT: D  154 MET cc_start: 0.8960 (mmm) cc_final: 0.8583 (mmm)
REVERT: D  344 MET cc_start: 0.7857 (ppp) cc_final: 0.7462 (ppp)
REVERT: D  719 ARG cc_start: 0.8755 (mtm-85) cc_final: 0.8266 (mtm-85)
REVERT: D  747 ASN cc_start: 0.8402 (t0) cc_final: 0.8054 (t0)
REVERT: D  794 GLU cc_start: 0.8676 (tm-30) cc_final: 0.8327 (pp20)
REVERT: D  992 LEU cc_start: 0.8406 (mm) cc_final: 0.8062 (mm)
REVERT: D 1209 MET cc_start: 0.7924 (mtm) cc_final: 0.7377 (mtm)
REVERT: D 1614 ASP cc_start: 0.8609 (OUTLIER) cc_final: 0.8331 (t0)
REVERT: D 1681 MET cc_start: 0.7656 (tmm) cc_final: 0.7414 (tmm)
REVERT: D 1689 MET cc_start: 0.7213 (tmm) cc_final: 0.6942 (mmm)
  outliers start: 28
  outliers final: 18
  residues processed: 253
  average time/residue: 0.1696
  time to fit residues: 71.7393
Evaluate side-chains
  236 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 215
  time to evaluate  : 1.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  236 ARG
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  765 LEU
Chi-restraints excluded: chain A residue  939 MET
Chi-restraints excluded: chain A residue 1355 CYS
Chi-restraints excluded: chain A residue 1374 LEU
Chi-restraints excluded: chain A residue 1405 THR
Chi-restraints excluded: chain D residue   42 LEU
Chi-restraints excluded: chain D residue  115 THR
Chi-restraints excluded: chain D residue  534 ASP
Chi-restraints excluded: chain D residue  770 LEU
Chi-restraints excluded: chain D residue 1292 TRP
Chi-restraints excluded: chain D residue 1614 ASP
Chi-restraints excluded: chain D residue 1714 LEU
Chi-restraints excluded: chain E residue  252 ASP
Chi-restraints excluded: chain E residue  264 THR
Chi-restraints excluded: chain E residue  281 VAL
Chi-restraints excluded: chain E residue  301 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 346
   random chunks:
   chunk 191 optimal weight:    0.9980
   chunk 323 optimal weight:    1.9990
   chunk 334 optimal weight:    7.9990
   chunk 199 optimal weight:    4.9990
   chunk 160 optimal weight:    8.9990
   chunk 313 optimal weight:   10.0000
   chunk 143 optimal weight:    0.6980
   chunk 138 optimal weight:    0.9980
   chunk 265 optimal weight:    6.9990
   chunk 315 optimal weight:    7.9990
   chunk 220 optimal weight:    3.9990
   overall best weight:    1.7384

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

Flipped N/Q/H residues before XYZ refinement:
** A  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 734 GLN
D 778 HIS
** D1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.086667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.064003 restraints weight = 127237.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.065852 restraints weight = 74368.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.066152 restraints weight = 47626.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.066556 restraints weight = 41197.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.066563 restraints weight = 37456.280|
|-----------------------------------------------------------------------------|
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.1428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.112  30334  Z= 0.127
  Angle     :  0.561   9.065  41488  Z= 0.288
  Chirality :  0.040   0.185   4733
  Planarity :  0.004   0.046   4953
  Dihedral  : 14.155 160.926   5192
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  3.47 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  :  9.76 %
    Favored  : 89.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.28 (0.15), residues: 3370
  helix:  0.95 (0.13), residues: 1605
  sheet: -0.72 (0.26), residues: 368
  loop : -0.34 (0.17), residues: 1397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 334 
 TYR   0.013   0.001   TYR A1468 
 PHE   0.016   0.001   PHE A1001 
 TRP   0.019   0.001   TRP D 814 
 HIS   0.006   0.001   HIS D 934 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 (30334)
  covalent geometry    : angle       0.56103 (41488)
  hydrogen bonds       : bond        0.04418 ( 1454)
  hydrogen bonds       : angle       4.66757 ( 4120)

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

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

  6740 Ramachandran restraints generated.
    3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6740 Ramachandran restraints generated.
    3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 234
  time to evaluate  : 0.791 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  344 MET cc_start: 0.8123 (mmm) cc_final: 0.7582 (mmm)
REVERT: A  362 PHE cc_start: 0.6371 (OUTLIER) cc_final: 0.5955 (m-10)
REVERT: A  531 TYR cc_start: 0.8650 (t80) cc_final: 0.8436 (t80)
REVERT: A  589 PHE cc_start: 0.7685 (t80) cc_final: 0.7428 (t80)
REVERT: A  829 TYR cc_start: 0.7792 (p90) cc_final: 0.6809 (p90)
REVERT: A  907 TYR cc_start: 0.7989 (m-80) cc_final: 0.7644 (m-80)
REVERT: A 1209 MET cc_start: 0.7719 (ptt) cc_final: 0.7307 (ptt)
REVERT: A 1343 TYR cc_start: 0.8008 (m-80) cc_final: 0.7661 (m-80)
REVERT: A 1371 GLU cc_start: 0.8112 (tt0) cc_final: 0.7893 (tt0)
REVERT: A 1417 MET cc_start: 0.1583 (tpt) cc_final: 0.1348 (tpt)
REVERT: C  218 MET cc_start: 0.8658 (ppp) cc_final: 0.8440 (ppp)
REVERT: D  208 MET cc_start: 0.7664 (mmm) cc_final: 0.7274 (mmp)
REVERT: D  212 MET cc_start: 0.9081 (ppp) cc_final: 0.8836 (ppp)
REVERT: D  238 ILE cc_start: 0.9477 (OUTLIER) cc_final: 0.9218 (mp)
REVERT: D  344 MET cc_start: 0.7856 (ppp) cc_final: 0.7402 (ppp)
REVERT: D  719 ARG cc_start: 0.8699 (mtm-85) cc_final: 0.8350 (mpp80)
REVERT: D  747 ASN cc_start: 0.8352 (t0) cc_final: 0.8027 (t0)
REVERT: D  794 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8322 (pp20)
REVERT: D  805 MET cc_start: 0.7627 (ppp) cc_final: 0.6983 (ppp)
REVERT: D  939 MET cc_start: 0.4118 (ppp) cc_final: 0.2268 (ptp)
REVERT: D  992 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8104 (mm)
REVERT: D 1016 LEU cc_start: 0.7787 (mm) cc_final: 0.7506 (mt)
REVERT: D 1209 MET cc_start: 0.7900 (mtm) cc_final: 0.7609 (mtm)
REVERT: D 1614 ASP cc_start: 0.8675 (OUTLIER) cc_final: 0.8405 (t0)
REVERT: D 1681 MET cc_start: 0.7710 (tmm) cc_final: 0.7370 (tmm)
REVERT: D 1689 MET cc_start: 0.7355 (tmm) cc_final: 0.7090 (mmm)
  outliers start: 35
  outliers final: 23
  residues processed: 255
  average time/residue: 0.1834
  time to fit residues: 77.7419
Evaluate side-chains
  245 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 218
  time to evaluate  : 1.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  362 PHE
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  765 LEU
Chi-restraints excluded: chain A residue  895 VAL
Chi-restraints excluded: chain A residue 1374 LEU
Chi-restraints excluded: chain C residue  264 THR
Chi-restraints excluded: chain D residue   42 LEU
Chi-restraints excluded: chain D residue  115 THR
Chi-restraints excluded: chain D residue  238 ILE
Chi-restraints excluded: chain D residue  504 LEU
Chi-restraints excluded: chain D residue  534 ASP
Chi-restraints excluded: chain D residue  770 LEU
Chi-restraints excluded: chain D residue  992 LEU
Chi-restraints excluded: chain D residue 1207 PHE
Chi-restraints excluded: chain D residue 1292 TRP
Chi-restraints excluded: chain D residue 1356 VAL
Chi-restraints excluded: chain D residue 1451 LEU
Chi-restraints excluded: chain D residue 1614 ASP
Chi-restraints excluded: chain D residue 1714 LEU
Chi-restraints excluded: chain E residue  252 ASP
Chi-restraints excluded: chain E residue  264 THR
Chi-restraints excluded: chain E residue  281 VAL
Chi-restraints excluded: chain E residue  301 HIS
Chi-restraints excluded: chain E residue  311 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 346
   random chunks:
   chunk 276 optimal weight:    0.0670
   chunk 128 optimal weight:    9.9990
   chunk 118 optimal weight:    0.8980
   chunk 289 optimal weight:    7.9990
   chunk 324 optimal weight:    9.9990
   chunk 13 optimal weight:    7.9990
   chunk 11 optimal weight:    8.9990
   chunk 47 optimal weight:   10.0000
   chunk 312 optimal weight:    8.9990
   chunk 309 optimal weight:    7.9990
   chunk 294 optimal weight:   10.0000
   overall best weight:    4.9924

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

Flipped N/Q/H residues before XYZ refinement:
** A  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 361 ASN
A 422 GLN
** A1433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1605 ASN
** D 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.084161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.061059 restraints weight = 127543.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.062704 restraints weight = 75778.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.063348 restraints weight = 48640.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.063618 restraints weight = 40562.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.063643 restraints weight = 36488.622|
|-----------------------------------------------------------------------------|
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.1871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.082  30334  Z= 0.248
  Angle     :  0.651  10.012  41488  Z= 0.338
  Chirality :  0.043   0.261   4733
  Planarity :  0.004   0.047   4953
  Dihedral  : 14.301 161.018   5192
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 11.76
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  4.45 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 11.07 %
    Favored  : 86.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.13 (0.14), residues: 3370
  helix:  0.66 (0.13), residues: 1617
  sheet: -1.06 (0.25), residues: 383
  loop : -0.55 (0.17), residues: 1370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 369 
 TYR   0.022   0.002   TYR A1468 
 PHE   0.017   0.002   PHE D 370 
 TRP   0.017   0.002   TRP D 814 
 HIS   0.009   0.001   HIS D1185 

Details of bonding type rmsd
  covalent geometry    : bond        0.00560 (30334)
  covalent geometry    : angle       0.65129 (41488)
  hydrogen bonds       : bond        0.04921 ( 1454)
  hydrogen bonds       : angle       4.90083 ( 4120)

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

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

  6740 Ramachandran restraints generated.
    3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6740 Ramachandran restraints generated.
    3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  281 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 218
  time to evaluate  : 1.446 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  317 LEU cc_start: 0.8593 (tp) cc_final: 0.8223 (tt)
REVERT: A  344 MET cc_start: 0.8105 (mmm) cc_final: 0.7594 (mmm)
REVERT: A  362 PHE cc_start: 0.6738 (OUTLIER) cc_final: 0.6381 (m-10)
REVERT: A  531 TYR cc_start: 0.8764 (t80) cc_final: 0.8508 (t80)
REVERT: A  849 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.8092 (mtp)
REVERT: A 1307 LEU cc_start: 0.9066 (mt) cc_final: 0.8760 (mp)
REVERT: B  352 LYS cc_start: 0.6840 (mmmt) cc_final: 0.6538 (mmmt)
REVERT: C  218 MET cc_start: 0.8776 (ppp) cc_final: 0.8538 (ppp)
REVERT: C  266 LYS cc_start: 0.8702 (mppt) cc_final: 0.8351 (mppt)
REVERT: D  208 MET cc_start: 0.7776 (mmm) cc_final: 0.7284 (mmp)
REVERT: D  212 MET cc_start: 0.9109 (ppp) cc_final: 0.8905 (ppp)
REVERT: D  238 ILE cc_start: 0.9540 (OUTLIER) cc_final: 0.9249 (mp)
REVERT: D  344 MET cc_start: 0.8139 (ppp) cc_final: 0.7647 (ppp)
REVERT: D  719 ARG cc_start: 0.8704 (mtm-85) cc_final: 0.8282 (mtm-85)
REVERT: D  747 ASN cc_start: 0.8464 (t0) cc_final: 0.8194 (t0)
REVERT: D  992 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8207 (mm)
REVERT: D  999 MET cc_start: 0.8737 (ptp) cc_final: 0.8395 (ptt)
REVERT: D 1029 MET cc_start: 0.8246 (mmm) cc_final: 0.7988 (mmm)
REVERT: D 1207 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.8189 (p90)
REVERT: D 1209 MET cc_start: 0.8041 (mtm) cc_final: 0.7545 (mtm)
REVERT: D 1681 MET cc_start: 0.7783 (tmm) cc_final: 0.7422 (tmm)
REVERT: D 1689 MET cc_start: 0.7312 (OUTLIER) cc_final: 0.6967 (mmm)
  outliers start: 63
  outliers final: 37
  residues processed: 262
  average time/residue: 0.1844
  time to fit residues: 81.3940
Evaluate side-chains
  250 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 207
  time to evaluate  : 1.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  362 PHE
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  596 VAL
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  625 MET
Chi-restraints excluded: chain A residue  765 LEU
Chi-restraints excluded: chain A residue  832 VAL
Chi-restraints excluded: chain A residue  849 MET
Chi-restraints excluded: chain A residue  895 VAL
Chi-restraints excluded: chain A residue 1206 VAL
Chi-restraints excluded: chain A residue 1355 CYS
Chi-restraints excluded: chain A residue 1405 THR
Chi-restraints excluded: chain C residue  247 TYR
Chi-restraints excluded: chain C residue  264 THR
Chi-restraints excluded: chain D residue   42 LEU
Chi-restraints excluded: chain D residue  115 THR
Chi-restraints excluded: chain D residue  176 ILE
Chi-restraints excluded: chain D residue  219 THR
Chi-restraints excluded: chain D residue  238 ILE
Chi-restraints excluded: chain D residue  504 LEU
Chi-restraints excluded: chain D residue  534 ASP
Chi-restraints excluded: chain D residue  770 LEU
Chi-restraints excluded: chain D residue  799 LEU
Chi-restraints excluded: chain D residue  992 LEU
Chi-restraints excluded: chain D residue 1185 HIS
Chi-restraints excluded: chain D residue 1205 ASP
Chi-restraints excluded: chain D residue 1207 PHE
Chi-restraints excluded: chain D residue 1292 TRP
Chi-restraints excluded: chain D residue 1356 VAL
Chi-restraints excluded: chain D residue 1451 LEU
Chi-restraints excluded: chain D residue 1541 ASN
Chi-restraints excluded: chain D residue 1689 MET
Chi-restraints excluded: chain D residue 1714 LEU
Chi-restraints excluded: chain E residue  252 ASP
Chi-restraints excluded: chain E residue  264 THR
Chi-restraints excluded: chain E residue  281 VAL
Chi-restraints excluded: chain E residue  289 VAL
Chi-restraints excluded: chain E residue  301 HIS
Chi-restraints excluded: chain E residue  311 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 346
   random chunks:
   chunk 156 optimal weight:    6.9990
   chunk 42 optimal weight:    7.9990
   chunk 263 optimal weight:   10.0000
   chunk 302 optimal weight:    0.8980
   chunk 188 optimal weight:    0.8980
   chunk 275 optimal weight:    6.9990
   chunk 190 optimal weight:    4.9990
   chunk 339 optimal weight:   10.0000
   chunk 328 optimal weight:   10.0000
   chunk 15 optimal weight:    7.9990
   chunk 122 optimal weight:    6.9990
   overall best weight:    4.1586

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

Flipped N/Q/H residues before XYZ refinement:
A  65 ASN
** A  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 428 ASN
** A1433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 109 ASN
** D 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.084332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.061181 restraints weight = 127822.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.062924 restraints weight = 74560.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.063423 restraints weight = 47276.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.063771 restraints weight = 40026.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.063834 restraints weight = 36429.729|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.2062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.078  30334  Z= 0.212
  Angle     :  0.630  15.340  41488  Z= 0.324
  Chirality :  0.042   0.368   4733
  Planarity :  0.004   0.046   4953
  Dihedral  : 14.301 159.722   5192
  Min Nonbonded Distance : 2.032

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  4.27 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 12.81 %
    Favored  : 84.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.22 (0.14), residues: 3370
  helix:  0.62 (0.13), residues: 1624
  sheet: -1.17 (0.24), residues: 384
  loop : -0.63 (0.17), residues: 1362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 496 
 TYR   0.024   0.002   TYR D1328 
 PHE   0.018   0.002   PHE A1001 
 TRP   0.019   0.002   TRP A1634 
 HIS   0.008   0.001   HIS D 934 

Details of bonding type rmsd
  covalent geometry    : bond        0.00481 (30334)
  covalent geometry    : angle       0.62956 (41488)
  hydrogen bonds       : bond        0.04623 ( 1454)
  hydrogen bonds       : angle       4.83490 ( 4120)

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

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

  6740 Ramachandran restraints generated.
    3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6740 Ramachandran restraints generated.
    3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 220
  time to evaluate  : 1.066 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 MET cc_start: 0.9071 (ttp) cc_final: 0.8728 (ttp)
REVERT: A  344 MET cc_start: 0.8117 (mmm) cc_final: 0.7645 (mmm)
REVERT: A  362 PHE cc_start: 0.6836 (OUTLIER) cc_final: 0.6496 (m-10)
REVERT: A  531 TYR cc_start: 0.8738 (t80) cc_final: 0.8520 (t80)
REVERT: A  849 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.8070 (mtp)
REVERT: A 1209 MET cc_start: 0.8010 (ptt) cc_final: 0.7572 (ptt)
REVERT: A 1307 LEU cc_start: 0.9059 (mt) cc_final: 0.8752 (mp)
REVERT: A 1417 MET cc_start: 0.1853 (tpt) cc_final: 0.1605 (tpt)
REVERT: B  352 LYS cc_start: 0.6900 (mmmt) cc_final: 0.6473 (mmmt)
REVERT: C  218 MET cc_start: 0.8738 (ppp) cc_final: 0.8472 (ppp)
REVERT: C  219 ARG cc_start: 0.8358 (tpt-90) cc_final: 0.8018 (tpp80)
REVERT: C  255 MET cc_start: 0.8756 (mpp) cc_final: 0.8511 (ptp)
REVERT: C  266 LYS cc_start: 0.8638 (mppt) cc_final: 0.8351 (mppt)
REVERT: D  208 MET cc_start: 0.7877 (mmm) cc_final: 0.7334 (mmp)
REVERT: D  238 ILE cc_start: 0.9513 (OUTLIER) cc_final: 0.9225 (mp)
REVERT: D  344 MET cc_start: 0.8165 (ppp) cc_final: 0.7704 (ppp)
REVERT: D  719 ARG cc_start: 0.8626 (mtm-85) cc_final: 0.8146 (mtm-85)
REVERT: D  747 ASN cc_start: 0.8331 (t0) cc_final: 0.7965 (t0)
REVERT: D  794 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8263 (pp20)
REVERT: D  992 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8217 (mm)
REVERT: D 1029 MET cc_start: 0.8308 (mmm) cc_final: 0.8073 (mmm)
REVERT: D 1209 MET cc_start: 0.8007 (mtm) cc_final: 0.7524 (mtm)
REVERT: D 1328 TYR cc_start: 0.6097 (OUTLIER) cc_final: 0.5653 (t80)
REVERT: D 1681 MET cc_start: 0.7865 (tmm) cc_final: 0.7568 (tmm)
REVERT: D 1689 MET cc_start: 0.7243 (OUTLIER) cc_final: 0.6960 (mmm)
  outliers start: 69
  outliers final: 48
  residues processed: 268
  average time/residue: 0.1800
  time to fit residues: 81.9048
Evaluate side-chains
  256 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 202
  time to evaluate  : 1.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  362 PHE
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  401 ILE
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  596 VAL
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  765 LEU
Chi-restraints excluded: chain A residue  787 GLU
Chi-restraints excluded: chain A residue  832 VAL
Chi-restraints excluded: chain A residue  849 MET
Chi-restraints excluded: chain A residue  895 VAL
Chi-restraints excluded: chain A residue  953 VAL
Chi-restraints excluded: chain A residue 1206 VAL
Chi-restraints excluded: chain A residue 1355 CYS
Chi-restraints excluded: chain A residue 1471 LEU
Chi-restraints excluded: chain A residue 1594 VAL
Chi-restraints excluded: chain B residue  344 ILE
Chi-restraints excluded: chain C residue  247 TYR
Chi-restraints excluded: chain C residue  264 THR
Chi-restraints excluded: chain D residue   42 LEU
Chi-restraints excluded: chain D residue  115 THR
Chi-restraints excluded: chain D residue  122 MET
Chi-restraints excluded: chain D residue  176 ILE
Chi-restraints excluded: chain D residue  219 THR
Chi-restraints excluded: chain D residue  238 ILE
Chi-restraints excluded: chain D residue  386 ILE
Chi-restraints excluded: chain D residue  504 LEU
Chi-restraints excluded: chain D residue  506 THR
Chi-restraints excluded: chain D residue  534 ASP
Chi-restraints excluded: chain D residue  770 LEU
Chi-restraints excluded: chain D residue  895 VAL
Chi-restraints excluded: chain D residue  992 LEU
Chi-restraints excluded: chain D residue 1185 HIS
Chi-restraints excluded: chain D residue 1205 ASP
Chi-restraints excluded: chain D residue 1292 TRP
Chi-restraints excluded: chain D residue 1328 TYR
Chi-restraints excluded: chain D residue 1356 VAL
Chi-restraints excluded: chain D residue 1421 VAL
Chi-restraints excluded: chain D residue 1451 LEU
Chi-restraints excluded: chain D residue 1514 CYS
Chi-restraints excluded: chain D residue 1541 ASN
Chi-restraints excluded: chain D residue 1689 MET
Chi-restraints excluded: chain D residue 1714 LEU
Chi-restraints excluded: chain E residue  252 ASP
Chi-restraints excluded: chain E residue  264 THR
Chi-restraints excluded: chain E residue  281 VAL
Chi-restraints excluded: chain E residue  289 VAL
Chi-restraints excluded: chain E residue  311 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 346
   random chunks:
   chunk 82 optimal weight:   10.0000
   chunk 332 optimal weight:    3.9990
   chunk 167 optimal weight:    6.9990
   chunk 86 optimal weight:    0.9980
   chunk 209 optimal weight:    2.9990
   chunk 282 optimal weight:    0.7980
   chunk 257 optimal weight:   30.0000
   chunk 18 optimal weight:    8.9990
   chunk 231 optimal weight:    2.9990
   chunk 283 optimal weight:    5.9990
   chunk 271 optimal weight:    6.9990
   overall best weight:    2.3586

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

Flipped N/Q/H residues before XYZ refinement:
** A  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 361 ASN
** A1433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.085314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.062323 restraints weight = 127354.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.064561 restraints weight = 70578.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.064779 restraints weight = 46977.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.065261 restraints weight = 37605.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.065299 restraints weight = 35491.863|
|-----------------------------------------------------------------------------|
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.2125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071  30334  Z= 0.145
  Angle     :  0.590  13.259  41488  Z= 0.300
  Chirality :  0.041   0.208   4733
  Planarity :  0.004   0.045   4953
  Dihedral  : 14.184 159.627   5192
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  4.09 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 13.34 %
    Favored  : 84.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.02 (0.14), residues: 3370
  helix:  0.82 (0.13), residues: 1616
  sheet: -1.11 (0.24), residues: 385
  loop : -0.56 (0.17), residues: 1369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 496 
 TYR   0.022   0.001   TYR D1328 
 PHE   0.018   0.001   PHE D 370 
 TRP   0.020   0.001   TRP A1634 
 HIS   0.007   0.001   HIS D 934 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (30334)
  covalent geometry    : angle       0.58965 (41488)
  hydrogen bonds       : bond        0.04267 ( 1454)
  hydrogen bonds       : angle       4.67051 ( 4120)

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

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

  6740 Ramachandran restraints generated.
    3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6740 Ramachandran restraints generated.
    3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 226
  time to evaluate  : 1.210 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  317 LEU cc_start: 0.8232 (tt) cc_final: 0.7963 (tp)
REVERT: A  322 MET cc_start: 0.9080 (ttp) cc_final: 0.8730 (ttp)
REVERT: A  344 MET cc_start: 0.8121 (mmm) cc_final: 0.7637 (mmm)
REVERT: A  362 PHE cc_start: 0.6751 (OUTLIER) cc_final: 0.6383 (m-10)
REVERT: A  849 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7991 (mtp)
REVERT: A  908 MET cc_start: 0.5478 (mmt) cc_final: 0.5143 (mmt)
REVERT: A  922 MET cc_start: 0.8527 (mmm) cc_final: 0.8259 (mmm)
REVERT: A 1209 MET cc_start: 0.7918 (ptt) cc_final: 0.7496 (ptt)
REVERT: A 1417 MET cc_start: 0.1952 (tpt) cc_final: 0.1717 (tpt)
REVERT: C  218 MET cc_start: 0.8674 (ppp) cc_final: 0.8435 (ppp)
REVERT: C  219 ARG cc_start: 0.8312 (tpt-90) cc_final: 0.7945 (tpp80)
REVERT: C  223 ARG cc_start: 0.8014 (ptt-90) cc_final: 0.7631 (tmm-80)
REVERT: C  258 MET cc_start: 0.8044 (ppp) cc_final: 0.7713 (ppp)
REVERT: C  266 LYS cc_start: 0.8641 (mppt) cc_final: 0.8352 (mppt)
REVERT: D  208 MET cc_start: 0.7854 (mmm) cc_final: 0.7326 (mmp)
REVERT: D  238 ILE cc_start: 0.9519 (OUTLIER) cc_final: 0.9229 (mp)
REVERT: D  344 MET cc_start: 0.8039 (ppp) cc_final: 0.7574 (ppp)
REVERT: D  620 MET cc_start: 0.7887 (mmp) cc_final: 0.7656 (mmm)
REVERT: D  719 ARG cc_start: 0.8629 (mtm-85) cc_final: 0.8179 (mtm-85)
REVERT: D  747 ASN cc_start: 0.8334 (t0) cc_final: 0.7963 (t0)
REVERT: D  794 GLU cc_start: 0.8592 (tm-30) cc_final: 0.8292 (pp20)
REVERT: D  805 MET cc_start: 0.7686 (ppp) cc_final: 0.7085 (ppp)
REVERT: D  939 MET cc_start: 0.4387 (ppp) cc_final: 0.2104 (mmt)
REVERT: D  992 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8008 (mm)
REVERT: D  995 ILE cc_start: 0.9405 (OUTLIER) cc_final: 0.9021 (tp)
REVERT: D 1002 LEU cc_start: 0.8953 (tt) cc_final: 0.8662 (tp)
REVERT: D 1029 MET cc_start: 0.8339 (mmm) cc_final: 0.8125 (mmm)
REVERT: D 1328 TYR cc_start: 0.6109 (OUTLIER) cc_final: 0.5644 (t80)
REVERT: D 1614 ASP cc_start: 0.8586 (OUTLIER) cc_final: 0.8172 (t0)
REVERT: D 1681 MET cc_start: 0.7925 (tmm) cc_final: 0.7629 (tmm)
REVERT: D 1689 MET cc_start: 0.7295 (OUTLIER) cc_final: 0.6990 (mmm)
  outliers start: 69
  outliers final: 50
  residues processed: 272
  average time/residue: 0.1696
  time to fit residues: 78.1267
Evaluate side-chains
  273 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 215
  time to evaluate  : 1.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  362 PHE
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  582 ILE
Chi-restraints excluded: chain A residue  596 VAL
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  765 LEU
Chi-restraints excluded: chain A residue  787 GLU
Chi-restraints excluded: chain A residue  832 VAL
Chi-restraints excluded: chain A residue  849 MET
Chi-restraints excluded: chain A residue  895 VAL
Chi-restraints excluded: chain A residue  953 VAL
Chi-restraints excluded: chain A residue 1355 CYS
Chi-restraints excluded: chain A residue 1374 LEU
Chi-restraints excluded: chain A residue 1461 THR
Chi-restraints excluded: chain A residue 1471 LEU
Chi-restraints excluded: chain A residue 1594 VAL
Chi-restraints excluded: chain A residue 1654 ILE
Chi-restraints excluded: chain B residue  344 ILE
Chi-restraints excluded: chain C residue  247 TYR
Chi-restraints excluded: chain D residue   42 LEU
Chi-restraints excluded: chain D residue  115 THR
Chi-restraints excluded: chain D residue  219 THR
Chi-restraints excluded: chain D residue  238 ILE
Chi-restraints excluded: chain D residue  322 MET
Chi-restraints excluded: chain D residue  386 ILE
Chi-restraints excluded: chain D residue  504 LEU
Chi-restraints excluded: chain D residue  506 THR
Chi-restraints excluded: chain D residue  534 ASP
Chi-restraints excluded: chain D residue  770 LEU
Chi-restraints excluded: chain D residue  799 LEU
Chi-restraints excluded: chain D residue  895 VAL
Chi-restraints excluded: chain D residue  992 LEU
Chi-restraints excluded: chain D residue  995 ILE
Chi-restraints excluded: chain D residue 1185 HIS
Chi-restraints excluded: chain D residue 1205 ASP
Chi-restraints excluded: chain D residue 1292 TRP
Chi-restraints excluded: chain D residue 1310 LEU
Chi-restraints excluded: chain D residue 1328 TYR
Chi-restraints excluded: chain D residue 1356 VAL
Chi-restraints excluded: chain D residue 1451 LEU
Chi-restraints excluded: chain D residue 1474 ILE
Chi-restraints excluded: chain D residue 1541 ASN
Chi-restraints excluded: chain D residue 1606 VAL
Chi-restraints excluded: chain D residue 1614 ASP
Chi-restraints excluded: chain D residue 1689 MET
Chi-restraints excluded: chain D residue 1714 LEU
Chi-restraints excluded: chain E residue  252 ASP
Chi-restraints excluded: chain E residue  281 VAL
Chi-restraints excluded: chain E residue  289 VAL
Chi-restraints excluded: chain E residue  301 HIS
Chi-restraints excluded: chain E residue  311 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 346
   random chunks:
   chunk 39 optimal weight:    0.9980
   chunk 305 optimal weight:    3.9990
   chunk 188 optimal weight:    7.9990
   chunk 258 optimal weight:    5.9990
   chunk 289 optimal weight:    5.9990
   chunk 79 optimal weight:    7.9990
   chunk 175 optimal weight:    4.9990
   chunk 145 optimal weight:    3.9990
   chunk 97 optimal weight:    0.0970
   chunk 4 optimal weight:    4.9990
   chunk 210 optimal weight:    4.9990
   overall best weight:    2.8184

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

Flipped N/Q/H residues before XYZ refinement:
** A  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 349 GLN
** D 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.085023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.061936 restraints weight = 127763.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.064450 restraints weight = 73253.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.064576 restraints weight = 45041.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.064937 restraints weight = 37685.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.064905 restraints weight = 35508.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.2236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070  30334  Z= 0.161
  Angle     :  0.599  14.591  41488  Z= 0.304
  Chirality :  0.041   0.322   4733
  Planarity :  0.004   0.052   4953
  Dihedral  : 14.111 159.770   5192
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  4.24 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 13.96 %
    Favored  : 83.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.03 (0.14), residues: 3370
  helix:  0.81 (0.13), residues: 1624
  sheet: -1.12 (0.24), residues: 379
  loop : -0.57 (0.17), residues: 1367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 496 
 TYR   0.024   0.001   TYR A 531 
 PHE   0.017   0.001   PHE D 370 
 TRP   0.018   0.001   TRP A1634 
 HIS   0.008   0.001   HIS A1305 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 (30334)
  covalent geometry    : angle       0.59882 (41488)
  hydrogen bonds       : bond        0.04283 ( 1454)
  hydrogen bonds       : angle       4.66910 ( 4120)

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

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

  6740 Ramachandran restraints generated.
    3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6740 Ramachandran restraints generated.
    3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 82
    poor density    : 216
  time to evaluate  : 1.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  236 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8428 (mpp80)
REVERT: A  322 MET cc_start: 0.9040 (ttp) cc_final: 0.8685 (ttp)
REVERT: A  344 MET cc_start: 0.8118 (mmm) cc_final: 0.7635 (mmm)
REVERT: A  360 MET cc_start: 0.8005 (tpt) cc_final: 0.7562 (mtm)
REVERT: A  362 PHE cc_start: 0.6807 (OUTLIER) cc_final: 0.6395 (m-10)
REVERT: A  908 MET cc_start: 0.5545 (mmt) cc_final: 0.5160 (mmt)
REVERT: A 1209 MET cc_start: 0.7958 (ptt) cc_final: 0.7533 (ptt)
REVERT: A 1343 TYR cc_start: 0.7932 (m-10) cc_final: 0.7257 (m-10)
REVERT: A 1417 MET cc_start: 0.2063 (tpt) cc_final: 0.1854 (tpt)
REVERT: C  218 MET cc_start: 0.8502 (ppp) cc_final: 0.8240 (ppp)
REVERT: C  219 ARG cc_start: 0.8352 (tpt-90) cc_final: 0.7946 (tpp80)
REVERT: D  208 MET cc_start: 0.7875 (mmm) cc_final: 0.7350 (mmp)
REVERT: D  238 ILE cc_start: 0.9507 (OUTLIER) cc_final: 0.9229 (mp)
REVERT: D  344 MET cc_start: 0.8101 (ppp) cc_final: 0.7642 (ppp)
REVERT: D  719 ARG cc_start: 0.8673 (mtm-85) cc_final: 0.8133 (mtm-85)
REVERT: D  747 ASN cc_start: 0.8326 (t0) cc_final: 0.7963 (t0)
REVERT: D  768 MET cc_start: 0.8751 (tpt) cc_final: 0.8413 (tpt)
REVERT: D  794 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8299 (pp20)
REVERT: D  805 MET cc_start: 0.7671 (ppp) cc_final: 0.7072 (ppp)
REVERT: D  852 PHE cc_start: 0.7138 (OUTLIER) cc_final: 0.6851 (m-10)
REVERT: D  939 MET cc_start: 0.4424 (ppp) cc_final: 0.2867 (ptp)
REVERT: D  992 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8020 (mm)
REVERT: D 1002 LEU cc_start: 0.8982 (tt) cc_final: 0.8740 (tp)
REVERT: D 1003 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7743 (mm)
REVERT: D 1259 ASP cc_start: 0.7962 (p0) cc_final: 0.7737 (m-30)
REVERT: D 1328 TYR cc_start: 0.6139 (OUTLIER) cc_final: 0.5574 (t80)
REVERT: D 1614 ASP cc_start: 0.8593 (OUTLIER) cc_final: 0.8205 (t0)
REVERT: D 1681 MET cc_start: 0.7918 (tmm) cc_final: 0.7587 (tmm)
REVERT: D 1689 MET cc_start: 0.7208 (OUTLIER) cc_final: 0.6901 (mmm)
  outliers start: 82
  outliers final: 62
  residues processed: 271
  average time/residue: 0.1838
  time to fit residues: 84.3817
Evaluate side-chains
  280 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 209
  time to evaluate  : 1.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  236 ARG
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  362 PHE
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  582 ILE
Chi-restraints excluded: chain A residue  596 VAL
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  765 LEU
Chi-restraints excluded: chain A residue  787 GLU
Chi-restraints excluded: chain A residue  832 VAL
Chi-restraints excluded: chain A residue  895 VAL
Chi-restraints excluded: chain A residue  933 VAL
Chi-restraints excluded: chain A residue  953 VAL
Chi-restraints excluded: chain A residue  999 MET
Chi-restraints excluded: chain A residue 1206 VAL
Chi-restraints excluded: chain A residue 1355 CYS
Chi-restraints excluded: chain A residue 1374 LEU
Chi-restraints excluded: chain A residue 1461 THR
Chi-restraints excluded: chain A residue 1471 LEU
Chi-restraints excluded: chain A residue 1594 VAL
Chi-restraints excluded: chain A residue 1654 ILE
Chi-restraints excluded: chain B residue  344 ILE
Chi-restraints excluded: chain C residue  247 TYR
Chi-restraints excluded: chain C residue  264 THR
Chi-restraints excluded: chain D residue   42 LEU
Chi-restraints excluded: chain D residue  115 THR
Chi-restraints excluded: chain D residue  122 MET
Chi-restraints excluded: chain D residue  219 THR
Chi-restraints excluded: chain D residue  238 ILE
Chi-restraints excluded: chain D residue  322 MET
Chi-restraints excluded: chain D residue  386 ILE
Chi-restraints excluded: chain D residue  418 VAL
Chi-restraints excluded: chain D residue  504 LEU
Chi-restraints excluded: chain D residue  506 THR
Chi-restraints excluded: chain D residue  534 ASP
Chi-restraints excluded: chain D residue  770 LEU
Chi-restraints excluded: chain D residue  799 LEU
Chi-restraints excluded: chain D residue  852 PHE
Chi-restraints excluded: chain D residue  895 VAL
Chi-restraints excluded: chain D residue  934 HIS
Chi-restraints excluded: chain D residue  992 LEU
Chi-restraints excluded: chain D residue 1003 LEU
Chi-restraints excluded: chain D residue 1185 HIS
Chi-restraints excluded: chain D residue 1205 ASP
Chi-restraints excluded: chain D residue 1206 VAL
Chi-restraints excluded: chain D residue 1292 TRP
Chi-restraints excluded: chain D residue 1310 LEU
Chi-restraints excluded: chain D residue 1328 TYR
Chi-restraints excluded: chain D residue 1348 PHE
Chi-restraints excluded: chain D residue 1356 VAL
Chi-restraints excluded: chain D residue 1421 VAL
Chi-restraints excluded: chain D residue 1451 LEU
Chi-restraints excluded: chain D residue 1474 ILE
Chi-restraints excluded: chain D residue 1514 CYS
Chi-restraints excluded: chain D residue 1541 ASN
Chi-restraints excluded: chain D residue 1606 VAL
Chi-restraints excluded: chain D residue 1614 ASP
Chi-restraints excluded: chain D residue 1689 MET
Chi-restraints excluded: chain D residue 1714 LEU
Chi-restraints excluded: chain E residue  252 ASP
Chi-restraints excluded: chain E residue  264 THR
Chi-restraints excluded: chain E residue  281 VAL
Chi-restraints excluded: chain E residue  289 VAL
Chi-restraints excluded: chain E residue  301 HIS
Chi-restraints excluded: chain E residue  311 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 346
   random chunks:
   chunk 148 optimal weight:    3.9990
   chunk 127 optimal weight:    3.9990
   chunk 67 optimal weight:    0.6980
   chunk 41 optimal weight:    8.9990
   chunk 199 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 123 optimal weight:    7.9990
   chunk 323 optimal weight:    7.9990
   chunk 31 optimal weight:    5.9990
   chunk 149 optimal weight:    0.8980
   chunk 319 optimal weight:    6.9990
   overall best weight:    2.5186

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

Flipped N/Q/H residues before XYZ refinement:
** A  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1509 ASN
** D 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.085238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.062187 restraints weight = 127855.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.064502 restraints weight = 70727.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.064695 restraints weight = 45882.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.064987 restraints weight = 37906.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.065123 restraints weight = 35611.491|
|-----------------------------------------------------------------------------|
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.2313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074  30334  Z= 0.150
  Angle     :  0.602  18.789  41488  Z= 0.302
  Chirality :  0.041   0.206   4733
  Planarity :  0.004   0.049   4953
  Dihedral  : 14.052 159.781   5192
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  4.21 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 14.38 %
    Favored  : 83.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.01 (0.14), residues: 3370
  helix:  0.84 (0.13), residues: 1625
  sheet: -1.12 (0.24), residues: 379
  loop : -0.56 (0.17), residues: 1366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 496 
 TYR   0.023   0.001   TYR A 531 
 PHE   0.020   0.001   PHE A 370 
 TRP   0.018   0.001   TRP A1634 
 HIS   0.006   0.001   HIS D 934 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (30334)
  covalent geometry    : angle       0.60159 (41488)
  hydrogen bonds       : bond        0.04199 ( 1454)
  hydrogen bonds       : angle       4.63076 ( 4120)

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

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

  6740 Ramachandran restraints generated.
    3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6740 Ramachandran restraints generated.
    3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 79
    poor density    : 219
  time to evaluate  : 1.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  154 MET cc_start: 0.8716 (ttt) cc_final: 0.8512 (ttp)
REVERT: A  236 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8431 (mpp80)
REVERT: A  322 MET cc_start: 0.9038 (ttp) cc_final: 0.8665 (ttp)
REVERT: A  344 MET cc_start: 0.8045 (mmm) cc_final: 0.7564 (mmm)
REVERT: A  360 MET cc_start: 0.7985 (tpt) cc_final: 0.7571 (mtm)
REVERT: A  362 PHE cc_start: 0.6891 (OUTLIER) cc_final: 0.6457 (m-10)
REVERT: A  922 MET cc_start: 0.8584 (mmm) cc_final: 0.8353 (mmm)
REVERT: A 1209 MET cc_start: 0.7901 (ptt) cc_final: 0.7434 (ptt)
REVERT: A 1343 TYR cc_start: 0.7875 (m-10) cc_final: 0.7243 (m-10)
REVERT: C  200 LYS cc_start: 0.9277 (tppt) cc_final: 0.8601 (mmtm)
REVERT: C  218 MET cc_start: 0.8521 (ppp) cc_final: 0.8264 (ppp)
REVERT: C  219 ARG cc_start: 0.8332 (tpt-90) cc_final: 0.7897 (tpp80)
REVERT: C  266 LYS cc_start: 0.8594 (mppt) cc_final: 0.8340 (mppt)
REVERT: D  208 MET cc_start: 0.7881 (mmm) cc_final: 0.7229 (mmp)
REVERT: D  238 ILE cc_start: 0.9523 (OUTLIER) cc_final: 0.9242 (mp)
REVERT: D  344 MET cc_start: 0.8102 (ppp) cc_final: 0.7642 (ppp)
REVERT: D  719 ARG cc_start: 0.8703 (mtm-85) cc_final: 0.8362 (mtm-85)
REVERT: D  747 ASN cc_start: 0.8286 (t0) cc_final: 0.7928 (t0)
REVERT: D  794 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8320 (pp20)
REVERT: D  805 MET cc_start: 0.7641 (ppp) cc_final: 0.7062 (ppp)
REVERT: D  852 PHE cc_start: 0.7172 (OUTLIER) cc_final: 0.6869 (m-10)
REVERT: D  939 MET cc_start: 0.4466 (ppp) cc_final: 0.2909 (ptp)
REVERT: D  992 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7952 (mm)
REVERT: D 1002 LEU cc_start: 0.8961 (tt) cc_final: 0.8725 (tp)
REVERT: D 1003 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7597 (mm)
REVERT: D 1259 ASP cc_start: 0.7936 (p0) cc_final: 0.7725 (m-30)
REVERT: D 1328 TYR cc_start: 0.6330 (OUTLIER) cc_final: 0.5661 (t80)
REVERT: D 1614 ASP cc_start: 0.8591 (OUTLIER) cc_final: 0.8169 (t0)
REVERT: D 1681 MET cc_start: 0.7891 (tmm) cc_final: 0.7555 (tmm)
REVERT: D 1689 MET cc_start: 0.7205 (OUTLIER) cc_final: 0.6918 (mmm)
REVERT: E  246 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7184 (pm20)
  outliers start: 79
  outliers final: 64
  residues processed: 277
  average time/residue: 0.1861
  time to fit residues: 86.9982
Evaluate side-chains
  287 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 213
  time to evaluate  : 1.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  236 ARG
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  362 PHE
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  582 ILE
Chi-restraints excluded: chain A residue  596 VAL
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  765 LEU
Chi-restraints excluded: chain A residue  787 GLU
Chi-restraints excluded: chain A residue  832 VAL
Chi-restraints excluded: chain A residue  895 VAL
Chi-restraints excluded: chain A residue  933 VAL
Chi-restraints excluded: chain A residue  953 VAL
Chi-restraints excluded: chain A residue 1206 VAL
Chi-restraints excluded: chain A residue 1355 CYS
Chi-restraints excluded: chain A residue 1374 LEU
Chi-restraints excluded: chain A residue 1395 ILE
Chi-restraints excluded: chain A residue 1461 THR
Chi-restraints excluded: chain A residue 1471 LEU
Chi-restraints excluded: chain A residue 1594 VAL
Chi-restraints excluded: chain A residue 1654 ILE
Chi-restraints excluded: chain B residue  344 ILE
Chi-restraints excluded: chain C residue  247 TYR
Chi-restraints excluded: chain C residue  264 THR
Chi-restraints excluded: chain D residue   42 LEU
Chi-restraints excluded: chain D residue  115 THR
Chi-restraints excluded: chain D residue  122 MET
Chi-restraints excluded: chain D residue  174 VAL
Chi-restraints excluded: chain D residue  176 ILE
Chi-restraints excluded: chain D residue  219 THR
Chi-restraints excluded: chain D residue  220 GLU
Chi-restraints excluded: chain D residue  238 ILE
Chi-restraints excluded: chain D residue  322 MET
Chi-restraints excluded: chain D residue  386 ILE
Chi-restraints excluded: chain D residue  418 VAL
Chi-restraints excluded: chain D residue  504 LEU
Chi-restraints excluded: chain D residue  506 THR
Chi-restraints excluded: chain D residue  534 ASP
Chi-restraints excluded: chain D residue  770 LEU
Chi-restraints excluded: chain D residue  799 LEU
Chi-restraints excluded: chain D residue  852 PHE
Chi-restraints excluded: chain D residue  895 VAL
Chi-restraints excluded: chain D residue  903 THR
Chi-restraints excluded: chain D residue  934 HIS
Chi-restraints excluded: chain D residue  992 LEU
Chi-restraints excluded: chain D residue 1003 LEU
Chi-restraints excluded: chain D residue 1185 HIS
Chi-restraints excluded: chain D residue 1205 ASP
Chi-restraints excluded: chain D residue 1206 VAL
Chi-restraints excluded: chain D residue 1239 THR
Chi-restraints excluded: chain D residue 1292 TRP
Chi-restraints excluded: chain D residue 1310 LEU
Chi-restraints excluded: chain D residue 1328 TYR
Chi-restraints excluded: chain D residue 1356 VAL
Chi-restraints excluded: chain D residue 1421 VAL
Chi-restraints excluded: chain D residue 1451 LEU
Chi-restraints excluded: chain D residue 1474 ILE
Chi-restraints excluded: chain D residue 1514 CYS
Chi-restraints excluded: chain D residue 1541 ASN
Chi-restraints excluded: chain D residue 1606 VAL
Chi-restraints excluded: chain D residue 1614 ASP
Chi-restraints excluded: chain D residue 1689 MET
Chi-restraints excluded: chain D residue 1714 LEU
Chi-restraints excluded: chain E residue  246 GLU
Chi-restraints excluded: chain E residue  252 ASP
Chi-restraints excluded: chain E residue  264 THR
Chi-restraints excluded: chain E residue  281 VAL
Chi-restraints excluded: chain E residue  289 VAL
Chi-restraints excluded: chain E residue  301 HIS
Chi-restraints excluded: chain E residue  311 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 346
   random chunks:
   chunk 320 optimal weight:    0.9990
   chunk 158 optimal weight:    3.9990
   chunk 219 optimal weight:    6.9990
   chunk 137 optimal weight:    1.9990
   chunk 251 optimal weight:   30.0000
   chunk 60 optimal weight:    1.9990
   chunk 278 optimal weight:    5.9990
   chunk 249 optimal weight:    6.9990
   chunk 220 optimal weight:    0.8980
   chunk 279 optimal weight:    3.9990
   chunk 237 optimal weight:    6.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 884 GLN
** A1433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 287 GLN
** D1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.085726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.062781 restraints weight = 127218.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.064996 restraints weight = 70768.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.065113 restraints weight = 44571.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.065532 restraints weight = 39355.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.065557 restraints weight = 36434.578|
|-----------------------------------------------------------------------------|
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.2360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071  30334  Z= 0.132
  Angle     :  0.599  16.773  41488  Z= 0.298
  Chirality :  0.040   0.195   4733
  Planarity :  0.004   0.048   4953
  Dihedral  : 13.979 159.889   5192
  Min Nonbonded Distance : 2.083

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.12 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 14.71 %
    Favored  : 82.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.09 (0.15), residues: 3370
  helix:  0.90 (0.13), residues: 1628
  sheet: -1.03 (0.24), residues: 380
  loop : -0.52 (0.17), residues: 1362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D1031 
 TYR   0.023   0.001   TYR A 531 
 PHE   0.017   0.001   PHE D 370 
 TRP   0.020   0.001   TRP A1634 
 HIS   0.006   0.001   HIS D 934 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (30334)
  covalent geometry    : angle       0.59945 (41488)
  hydrogen bonds       : bond        0.04076 ( 1454)
  hydrogen bonds       : angle       4.56980 ( 4120)

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

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

  6740 Ramachandran restraints generated.
    3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6740 Ramachandran restraints generated.
    3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 226
  time to evaluate  : 1.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 MET cc_start: 0.9020 (ttp) cc_final: 0.8694 (ttp)
REVERT: A  344 MET cc_start: 0.8032 (mmm) cc_final: 0.7551 (mmm)
REVERT: A  360 MET cc_start: 0.7950 (tpt) cc_final: 0.7655 (mtm)
REVERT: A  362 PHE cc_start: 0.6973 (OUTLIER) cc_final: 0.6354 (m-10)
REVERT: A  907 TYR cc_start: 0.8192 (m-80) cc_final: 0.7717 (m-80)
REVERT: A  922 MET cc_start: 0.8566 (mmm) cc_final: 0.8304 (mmm)
REVERT: A  939 MET cc_start: 0.6935 (mmm) cc_final: 0.6395 (mmm)
REVERT: A 1209 MET cc_start: 0.7879 (ptt) cc_final: 0.7410 (ptt)
REVERT: A 1343 TYR cc_start: 0.7915 (m-10) cc_final: 0.7273 (m-10)
REVERT: C  200 LYS cc_start: 0.9270 (tppt) cc_final: 0.8890 (mttm)
REVERT: C  218 MET cc_start: 0.8473 (ppp) cc_final: 0.8194 (ppp)
REVERT: C  219 ARG cc_start: 0.8281 (tpt-90) cc_final: 0.7892 (tpp80)
REVERT: C  223 ARG cc_start: 0.8454 (ttp-170) cc_final: 0.8097 (tmm-80)
REVERT: C  266 LYS cc_start: 0.8555 (mppt) cc_final: 0.8293 (mppt)
REVERT: D  208 MET cc_start: 0.7884 (mmm) cc_final: 0.7227 (mmp)
REVERT: D  238 ILE cc_start: 0.9495 (OUTLIER) cc_final: 0.9210 (mp)
REVERT: D  344 MET cc_start: 0.8051 (ppp) cc_final: 0.7592 (ppp)
REVERT: D  719 ARG cc_start: 0.8727 (mtm-85) cc_final: 0.8497 (mtm-85)
REVERT: D  747 ASN cc_start: 0.8290 (t0) cc_final: 0.7925 (t0)
REVERT: D  794 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8337 (pp20)
REVERT: D  805 MET cc_start: 0.7606 (ppp) cc_final: 0.7030 (ppp)
REVERT: D  852 PHE cc_start: 0.7119 (OUTLIER) cc_final: 0.6778 (m-10)
REVERT: D  992 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7964 (mm)
REVERT: D 1003 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7464 (mm)
REVERT: D 1328 TYR cc_start: 0.6340 (OUTLIER) cc_final: 0.5629 (t80)
REVERT: D 1614 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.8149 (t0)
REVERT: D 1681 MET cc_start: 0.7873 (tmm) cc_final: 0.7538 (tmm)
REVERT: D 1689 MET cc_start: 0.7214 (OUTLIER) cc_final: 0.6878 (mmm)
REVERT: E  246 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7174 (pm20)
  outliers start: 73
  outliers final: 56
  residues processed: 280
  average time/residue: 0.1819
  time to fit residues: 86.1732
Evaluate side-chains
  282 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 217
  time to evaluate  : 1.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  362 PHE
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  596 VAL
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  765 LEU
Chi-restraints excluded: chain A residue  787 GLU
Chi-restraints excluded: chain A residue  832 VAL
Chi-restraints excluded: chain A residue  895 VAL
Chi-restraints excluded: chain A residue  933 VAL
Chi-restraints excluded: chain A residue  953 VAL
Chi-restraints excluded: chain A residue 1206 VAL
Chi-restraints excluded: chain A residue 1355 CYS
Chi-restraints excluded: chain A residue 1374 LEU
Chi-restraints excluded: chain A residue 1471 LEU
Chi-restraints excluded: chain A residue 1594 VAL
Chi-restraints excluded: chain A residue 1654 ILE
Chi-restraints excluded: chain B residue  344 ILE
Chi-restraints excluded: chain C residue  247 TYR
Chi-restraints excluded: chain C residue  264 THR
Chi-restraints excluded: chain D residue   42 LEU
Chi-restraints excluded: chain D residue  115 THR
Chi-restraints excluded: chain D residue  122 MET
Chi-restraints excluded: chain D residue  174 VAL
Chi-restraints excluded: chain D residue  219 THR
Chi-restraints excluded: chain D residue  220 GLU
Chi-restraints excluded: chain D residue  238 ILE
Chi-restraints excluded: chain D residue  322 MET
Chi-restraints excluded: chain D residue  386 ILE
Chi-restraints excluded: chain D residue  418 VAL
Chi-restraints excluded: chain D residue  504 LEU
Chi-restraints excluded: chain D residue  506 THR
Chi-restraints excluded: chain D residue  534 ASP
Chi-restraints excluded: chain D residue  770 LEU
Chi-restraints excluded: chain D residue  799 LEU
Chi-restraints excluded: chain D residue  852 PHE
Chi-restraints excluded: chain D residue  895 VAL
Chi-restraints excluded: chain D residue  903 THR
Chi-restraints excluded: chain D residue  934 HIS
Chi-restraints excluded: chain D residue  992 LEU
Chi-restraints excluded: chain D residue 1003 LEU
Chi-restraints excluded: chain D residue 1185 HIS
Chi-restraints excluded: chain D residue 1206 VAL
Chi-restraints excluded: chain D residue 1292 TRP
Chi-restraints excluded: chain D residue 1310 LEU
Chi-restraints excluded: chain D residue 1328 TYR
Chi-restraints excluded: chain D residue 1356 VAL
Chi-restraints excluded: chain D residue 1421 VAL
Chi-restraints excluded: chain D residue 1451 LEU
Chi-restraints excluded: chain D residue 1474 ILE
Chi-restraints excluded: chain D residue 1514 CYS
Chi-restraints excluded: chain D residue 1606 VAL
Chi-restraints excluded: chain D residue 1614 ASP
Chi-restraints excluded: chain D residue 1689 MET
Chi-restraints excluded: chain D residue 1714 LEU
Chi-restraints excluded: chain E residue  246 GLU
Chi-restraints excluded: chain E residue  252 ASP
Chi-restraints excluded: chain E residue  281 VAL
Chi-restraints excluded: chain E residue  289 VAL
Chi-restraints excluded: chain E residue  301 HIS
Chi-restraints excluded: chain E residue  311 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 346
   random chunks:
   chunk 198 optimal weight:    0.8980
   chunk 71 optimal weight:    2.9990
   chunk 113 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   chunk 95 optimal weight:   10.0000
   chunk 204 optimal weight:    1.9990
   chunk 240 optimal weight:    5.9990
   chunk 18 optimal weight:    1.9990
   chunk 63 optimal weight:   20.0000
   chunk 88 optimal weight:    4.9990
   chunk 145 optimal weight:    0.9980
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
** A  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.086256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.063310 restraints weight = 126537.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.065549 restraints weight = 68061.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.065885 restraints weight = 46319.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.066347 restraints weight = 34828.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.066421 restraints weight = 33109.318|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.2430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067  30334  Z= 0.117
  Angle     :  0.602  14.072  41488  Z= 0.298
  Chirality :  0.040   0.183   4733
  Planarity :  0.004   0.049   4953
  Dihedral  : 13.922 160.079   5192
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.68 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 15.17 %
    Favored  : 82.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.20 (0.15), residues: 3370
  helix:  0.98 (0.13), residues: 1627
  sheet: -0.92 (0.25), residues: 377
  loop : -0.47 (0.17), residues: 1366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 998 
 TYR   0.023   0.001   TYR A 531 
 PHE   0.023   0.001   PHE A 370 
 TRP   0.022   0.001   TRP A1634 
 HIS   0.006   0.001   HIS D 934 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (30334)
  covalent geometry    : angle       0.60172 (41488)
  hydrogen bonds       : bond        0.03971 ( 1454)
  hydrogen bonds       : angle       4.50454 ( 4120)

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

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

  6740 Ramachandran restraints generated.
    3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6740 Ramachandran restraints generated.
    3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 230
  time to evaluate  : 1.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 MET cc_start: 0.9024 (ttp) cc_final: 0.8701 (ttp)
REVERT: A  344 MET cc_start: 0.8033 (mmm) cc_final: 0.7549 (mmm)
REVERT: A  360 MET cc_start: 0.7980 (tpt) cc_final: 0.7717 (mtm)
REVERT: A  362 PHE cc_start: 0.6912 (OUTLIER) cc_final: 0.6300 (m-10)
REVERT: A  922 MET cc_start: 0.8630 (mmm) cc_final: 0.8346 (mmm)
REVERT: A 1209 MET cc_start: 0.7862 (ptt) cc_final: 0.7358 (ptt)
REVERT: A 1343 TYR cc_start: 0.7809 (m-10) cc_final: 0.7124 (m-10)
REVERT: A 1417 MET cc_start: 0.1683 (tpt) cc_final: 0.1094 (tpt)
REVERT: C  200 LYS cc_start: 0.9264 (tppt) cc_final: 0.8871 (mttm)
REVERT: C  218 MET cc_start: 0.8294 (ppp) cc_final: 0.8065 (ppp)
REVERT: C  219 ARG cc_start: 0.8265 (tpt-90) cc_final: 0.7892 (tpp80)
REVERT: C  223 ARG cc_start: 0.8130 (ttp-170) cc_final: 0.7623 (ttp-170)
REVERT: C  266 LYS cc_start: 0.8498 (mppt) cc_final: 0.8255 (mppt)
REVERT: D   75 MET cc_start: 0.8151 (ttp) cc_final: 0.7940 (tpp)
REVERT: D  208 MET cc_start: 0.7844 (mmm) cc_final: 0.7181 (mmp)
REVERT: D  238 ILE cc_start: 0.9491 (OUTLIER) cc_final: 0.9207 (mp)
REVERT: D  344 MET cc_start: 0.8018 (ppp) cc_final: 0.7548 (ppp)
REVERT: D  424 MET cc_start: 0.7720 (ttm) cc_final: 0.7491 (ttt)
REVERT: D  719 ARG cc_start: 0.8757 (mtm-85) cc_final: 0.8462 (mtm-85)
REVERT: D  747 ASN cc_start: 0.8270 (t0) cc_final: 0.7911 (t0)
REVERT: D  765 LEU cc_start: 0.8282 (mt) cc_final: 0.7695 (pp)
REVERT: D  794 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8355 (pp20)
REVERT: D  805 MET cc_start: 0.7576 (ppp) cc_final: 0.6986 (ppp)
REVERT: D  852 PHE cc_start: 0.7057 (OUTLIER) cc_final: 0.6719 (m-10)
REVERT: D  992 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7941 (mm)
REVERT: D 1002 LEU cc_start: 0.8930 (tt) cc_final: 0.8386 (pp)
REVERT: D 1003 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7323 (mm)
REVERT: D 1328 TYR cc_start: 0.6329 (OUTLIER) cc_final: 0.5629 (t80)
REVERT: D 1614 ASP cc_start: 0.8636 (OUTLIER) cc_final: 0.8171 (t0)
REVERT: D 1681 MET cc_start: 0.7894 (tmm) cc_final: 0.7567 (tmm)
REVERT: D 1689 MET cc_start: 0.7196 (OUTLIER) cc_final: 0.6872 (mmm)
REVERT: E  246 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7126 (pm20)
REVERT: E  256 ASP cc_start: 0.7923 (t0) cc_final: 0.7682 (t0)
  outliers start: 65
  outliers final: 52
  residues processed: 277
  average time/residue: 0.1820
  time to fit residues: 85.3891
Evaluate side-chains
  283 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 222
  time to evaluate  : 1.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  211 VAL
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  362 PHE
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  596 VAL
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  618 ILE
Chi-restraints excluded: chain A residue  765 LEU
Chi-restraints excluded: chain A residue  832 VAL
Chi-restraints excluded: chain A residue  895 VAL
Chi-restraints excluded: chain A residue  933 VAL
Chi-restraints excluded: chain A residue 1206 VAL
Chi-restraints excluded: chain A residue 1355 CYS
Chi-restraints excluded: chain A residue 1471 LEU
Chi-restraints excluded: chain A residue 1594 VAL
Chi-restraints excluded: chain A residue 1654 ILE
Chi-restraints excluded: chain B residue  344 ILE
Chi-restraints excluded: chain C residue  247 TYR
Chi-restraints excluded: chain C residue  264 THR
Chi-restraints excluded: chain D residue   42 LEU
Chi-restraints excluded: chain D residue  115 THR
Chi-restraints excluded: chain D residue  122 MET
Chi-restraints excluded: chain D residue  174 VAL
Chi-restraints excluded: chain D residue  219 THR
Chi-restraints excluded: chain D residue  220 GLU
Chi-restraints excluded: chain D residue  238 ILE
Chi-restraints excluded: chain D residue  322 MET
Chi-restraints excluded: chain D residue  418 VAL
Chi-restraints excluded: chain D residue  504 LEU
Chi-restraints excluded: chain D residue  506 THR
Chi-restraints excluded: chain D residue  534 ASP
Chi-restraints excluded: chain D residue  770 LEU
Chi-restraints excluded: chain D residue  799 LEU
Chi-restraints excluded: chain D residue  852 PHE
Chi-restraints excluded: chain D residue  895 VAL
Chi-restraints excluded: chain D residue  903 THR
Chi-restraints excluded: chain D residue  934 HIS
Chi-restraints excluded: chain D residue  992 LEU
Chi-restraints excluded: chain D residue 1003 LEU
Chi-restraints excluded: chain D residue 1206 VAL
Chi-restraints excluded: chain D residue 1239 THR
Chi-restraints excluded: chain D residue 1292 TRP
Chi-restraints excluded: chain D residue 1310 LEU
Chi-restraints excluded: chain D residue 1328 TYR
Chi-restraints excluded: chain D residue 1356 VAL
Chi-restraints excluded: chain D residue 1421 VAL
Chi-restraints excluded: chain D residue 1451 LEU
Chi-restraints excluded: chain D residue 1474 ILE
Chi-restraints excluded: chain D residue 1606 VAL
Chi-restraints excluded: chain D residue 1614 ASP
Chi-restraints excluded: chain D residue 1689 MET
Chi-restraints excluded: chain D residue 1714 LEU
Chi-restraints excluded: chain E residue  246 GLU
Chi-restraints excluded: chain E residue  252 ASP
Chi-restraints excluded: chain E residue  264 THR
Chi-restraints excluded: chain E residue  281 VAL
Chi-restraints excluded: chain E residue  289 VAL
Chi-restraints excluded: chain E residue  301 HIS
Chi-restraints excluded: chain E residue  311 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 346
   random chunks:
   chunk 296 optimal weight:    6.9990
   chunk 278 optimal weight:    0.8980
   chunk 336 optimal weight:    0.6980
   chunk 213 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 61 optimal weight:    6.9990
   chunk 16 optimal weight:    7.9990
   chunk 57 optimal weight:    0.9990
   chunk 234 optimal weight:    0.0570
   chunk 194 optimal weight:    3.9990
   chunk 1 optimal weight:    8.9990
   overall best weight:    1.3302

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

Flipped N/Q/H residues before XYZ refinement:
** A1433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 301 HIS
** D1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.086556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.063513 restraints weight = 127257.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.065965 restraints weight = 67850.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.066238 restraints weight = 45466.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.066575 restraints weight = 34747.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.066626 restraints weight = 32449.730|
|-----------------------------------------------------------------------------|
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.2489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  30334  Z= 0.114
  Angle     :  0.594  15.689  41488  Z= 0.294
  Chirality :  0.040   0.180   4733
  Planarity :  0.004   0.049   4953
  Dihedral  : 13.887 160.328   5192
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.74 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 15.43 %
    Favored  : 82.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.24 (0.15), residues: 3370
  helix:  0.99 (0.13), residues: 1633
  sheet: -0.79 (0.25), residues: 371
  loop : -0.47 (0.17), residues: 1366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D1031 
 TYR   0.034   0.001   TYR A 521 
 PHE   0.017   0.001   PHE D 370 
 TRP   0.021   0.001   TRP A1634 
 HIS   0.007   0.001   HIS D 934 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 (30334)
  covalent geometry    : angle       0.59364 (41488)
  hydrogen bonds       : bond        0.03902 ( 1454)
  hydrogen bonds       : angle       4.47627 ( 4120)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4992.58 seconds
wall clock time: 87 minutes 45.03 seconds (5265.03 seconds total)