Starting phenix.real_space_refine
on Wed Mar  4 12:40:17 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zgk_14708/03_2026/7zgk_14708_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zgk_14708/03_2026/7zgk_14708.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.59
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zgk_14708/03_2026/7zgk_14708.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zgk_14708/03_2026/7zgk_14708.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zgk_14708/03_2026/7zgk_14708_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zgk_14708/03_2026/7zgk_14708_neut.cif"
  }
  resolution = 3.59
  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=  -0.001 sd=   0.024
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      56      5.16       5
     C    8656      2.51       5
     N    2300      2.21       5
     O    2627      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13639
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4907
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 630, 4907
          Classifications: {'peptide': 630}
          Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 593}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 7197
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 901, 7197
          Classifications: {'peptide': 901}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 39, 'TRANS': 861}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 1535
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 192, 1535
          Classifications: {'peptide': 192}
          Link IDs: {'PTRANS': 4, 'TRANS': 187}
          Chain breaks: 2
  Time building chain proxies: 2.45, per 1000 atoms: 0.18
  Number of scatterers: 13639
  At special positions: 0
  Unit cell: (83.628, 132.48, 185.472, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      56     16.00
     O    2627      8.00
     N    2300      7.00
     C    8656      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 627 " - pdb=" SG  CYS A 662 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 873 " - pdb=" SG  CYS B1513 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1101 " - pdb=" SG  CYS B1158 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1358 " - pdb=" SG  CYS B1489 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1389 " - pdb=" SG  CYS B1458 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1506 " - pdb=" SG  CYS B1511 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1518 " - pdb=" SG  CYS B1590 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1537 " - pdb=" SG  CYS B1661 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1637 " - pdb=" SG  CYS B1646 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.93
  Conformation dependent library (CDL) restraints added in 559.3 milliseconds
  

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3246

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 25 sheets defined
      29.1% alpha, 29.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.51
  Creating SS restraints...
    Processing helix  chain 'A' and resid 77 through 81
    Processing helix  chain 'A' and resid 285 through 288
    Processing helix  chain 'A' and resid 303 through 311
    Processing helix  chain 'A' and resid 315 through 320
      removed outlier: 3.683A  pdb=" N   VAL A 320 " --> pdb=" O   GLU A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 452
      removed outlier: 3.779A  pdb=" N   ASN A 451 " --> pdb=" O   THR A 448 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   SER A 452 " --> pdb=" O   VAL A 449 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 448 through 452'
    Processing helix  chain 'A' and resid 480 through 484
      removed outlier: 3.536A  pdb=" N   GLU A 484 " --> pdb=" O   ARG A 481 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 600 through 606
      removed outlier: 3.867A  pdb=" N   LEU A 605 " --> pdb=" O   GLY A 601 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ASN A 606 " --> pdb=" O   VAL A 602 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 612 through 623
    Processing helix  chain 'A' and resid 634 through 643
    Processing helix  chain 'B' and resid 997 through 1004
      removed outlier: 3.586A  pdb=" N   LEU B1000 " --> pdb=" O   ALA B 997 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   LYS B1001 " --> pdb=" O   GLU B 998 " (cutoff:3.500A)
      removed outlier: 4.983A  pdb=" N   HIS B1002 " --> pdb=" O   ARG B 999 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1011 through 1032
      Proline residue:  B1020  - end of helix
    Processing helix  chain 'B' and resid 1033 through 1038
    Processing helix  chain 'B' and resid 1040 through 1059
      removed outlier: 3.737A  pdb=" N   GLY B1044 " --> pdb=" O   GLU B1040 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   PHE B1059 " --> pdb=" O   GLN B1055 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1075 through 1089
      removed outlier: 3.594A  pdb=" N   LEU B1088 " --> pdb=" O   LYS B1084 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1096 through 1112
      removed outlier: 3.551A  pdb=" N   LEU B1100 " --> pdb=" O   ASP B1096 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   LYS B1111 " --> pdb=" O   LEU B1107 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1130 through 1134
    Processing helix  chain 'B' and resid 1138 through 1156
      removed outlier: 3.654A  pdb=" N   ALA B1142 " --> pdb=" O   GLU B1138 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   THR B1144 " --> pdb=" O   ASP B1140 " (cutoff:3.500A)
      removed outlier: 4.428A  pdb=" N   ASP B1156 " --> pdb=" O   GLN B1152 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1164 through 1179
      removed outlier: 3.926A  pdb=" N   ASN B1179 " --> pdb=" O   PHE B1175 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1180 through 1183
    Processing helix  chain 'B' and resid 1185 through 1198
      removed outlier: 3.686A  pdb=" N   GLN B1198 " --> pdb=" O   TYR B1194 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1204 through 1213
    Processing helix  chain 'B' and resid 1214 through 1218
      removed outlier: 3.623A  pdb=" N   LYS B1217 " --> pdb=" O   ALA B1214 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   ASN B1218 " --> pdb=" O   LYS B1215 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 1214 through 1218'
    Processing helix  chain 'B' and resid 1225 through 1244
      removed outlier: 3.566A  pdb=" N   ASN B1229 " --> pdb=" O   LYS B1225 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1248 through 1259
      removed outlier: 4.158A  pdb=" N   VAL B1252 " --> pdb=" O   PHE B1248 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1268 through 1285
    Processing helix  chain 'B' and resid 1414 through 1423
      removed outlier: 3.963A  pdb=" N   ASN B1423 " --> pdb=" O   LYS B1419 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1430 through 1435
    Processing helix  chain 'B' and resid 1528 through 1536
    Processing helix  chain 'B' and resid 1588 through 1594
      removed outlier: 4.294A  pdb=" N   GLU B1592 " --> pdb=" O   ILE B1588 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ALA B1593 " --> pdb=" O   LYS B1589 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1639 through 1659
      removed outlier: 4.511A  pdb=" N   LYS B1644 " --> pdb=" O   GLU B1640 " (cutoff:3.500A)
      removed outlier: 4.633A  pdb=" N   GLN B1645 " --> pdb=" O   GLU B1641 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 36 through 55
    Processing helix  chain 'C' and resid 55 through 63
      removed outlier: 3.521A  pdb=" N   ASP C  62 " --> pdb=" O   GLN C  58 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 65 through 85
      removed outlier: 3.928A  pdb=" N   GLY C  69 " --> pdb=" O   GLN C  65 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   PHE C  73 " --> pdb=" O   GLY C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 92 through 97
      removed outlier: 3.649A  pdb=" N   ALA C  96 " --> pdb=" O   ASP C  93 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 99 through 119
      removed outlier: 3.572A  pdb=" N   GLU C 104 " --> pdb=" O   ASP C 100 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   LYS C 105 " --> pdb=" O   SER C 101 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   LYS C 119 " --> pdb=" O   ASP C 115 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 120 through 145
      removed outlier: 3.569A  pdb=" N   ALA C 124 " --> pdb=" O   GLN C 120 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 203 through 211
      removed outlier: 3.566A  pdb=" N   GLU C 206 " --> pdb=" O   THR C 203 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   TYR C 209 " --> pdb=" O   GLU C 206 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 215 through 226
      removed outlier: 4.372A  pdb=" N   ALA C 219 " --> pdb=" O   ALA C 215 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 260 through 300
      removed outlier: 3.722A  pdb=" N   THR C 264 " --> pdb=" O   PRO C 260 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   VAL C 265 " --> pdb=" O   TYR C 261 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   GLU C 266 " --> pdb=" O   LYS C 262 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   GLY C 287 " --> pdb=" O   ASP C 283 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   TYR C 288 " --> pdb=" O   ALA C 284 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   THR C 291 " --> pdb=" O   GLY C 287 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   ALA C 292 " --> pdb=" O   TYR C 288 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   TYR C 293 " --> pdb=" O   ALA C 289 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 304 through 312
      removed outlier: 3.662A  pdb=" N   VAL C 308 " --> pdb=" O   PRO C 304 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 89
      removed outlier: 8.789A  pdb=" N   THR A  41 " --> pdb=" O   PRO A  31 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 35
      removed outlier: 6.433A  pdb=" N   LEU A  34 " --> pdb=" O   SER A 124 " (cutoff:3.500A)
      removed outlier: 4.521A  pdb=" N   SER A  70 " --> pdb=" O   VAL A  59 " (cutoff:3.500A)
      removed outlier: 7.671A  pdb=" N   ASP A  61 " --> pdb=" O   VAL A  68 " (cutoff:3.500A)
      removed outlier: 7.773A  pdb=" N   VAL A  68 " --> pdb=" O   ASP A  61 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 134
    Processing sheet with id=AA4, first strand: chain 'A' and resid 138 through 139
      removed outlier: 6.205A  pdb=" N   VAL A 163 " --> pdb=" O   SER A 179 " (cutoff:3.500A)
      removed outlier: 4.537A  pdb=" N   SER A 179 " --> pdb=" O   VAL A 163 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   VAL A 165 " --> pdb=" O   GLN A 177 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   GLN A 177 " --> pdb=" O   VAL A 165 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   ILE A 167 " --> pdb=" O   VAL A 175 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 232 through 238
    Processing sheet with id=AA6, first strand: chain 'A' and resid 282 through 283
    Processing sheet with id=AA7, first strand: chain 'A' and resid 282 through 283
      removed outlier: 7.085A  pdb=" N   VAL A 326 " --> pdb=" O   SER A 344 " (cutoff:3.500A)
      removed outlier: 5.097A  pdb=" N   SER A 344 " --> pdb=" O   VAL A 326 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   ALA A 328 " --> pdb=" O   GLU A 342 " (cutoff:3.500A)
      removed outlier: 4.798A  pdb=" N   GLU A 342 " --> pdb=" O   ALA A 328 " (cutoff:3.500A)
      removed outlier: 7.238A  pdb=" N   VAL A 330 " --> pdb=" O   GLN A 340 " (cutoff:3.500A)
      removed outlier: 5.606A  pdb=" N   GLN A 340 " --> pdb=" O   VAL A 330 " (cutoff:3.500A)
      removed outlier: 7.832A  pdb=" N   LEU A 332 " --> pdb=" O   MET A 338 " (cutoff:3.500A)
      removed outlier: 7.585A  pdb=" N   MET A 338 " --> pdb=" O   LEU A 332 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 356
    Processing sheet with id=AA9, first strand: chain 'A' and resid 363 through 364
      removed outlier: 3.625A  pdb=" N   ARG A 425 " --> pdb=" O   ALA A 390 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   ALA A 390 " --> pdb=" O   ARG A 425 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   VAL A 389 " --> pdb=" O   SER A 399 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   SER A 399 " --> pdb=" O   VAL A 389 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 455 through 459
    Processing sheet with id=AB2, first strand: chain 'A' and resid 500 through 507
      removed outlier: 3.702A  pdb=" N   LYS A 502 " --> pdb=" O   ILE A 494 " (cutoff:3.500A)
      removed outlier: 7.644A  pdb=" N   TYR A 489 " --> pdb=" O   THR A 536 " (cutoff:3.500A)
      removed outlier: 5.865A  pdb=" N   THR A 536 " --> pdb=" O   TYR A 489 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   PHE A 529 " --> pdb=" O   VAL A 553 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 564 through 567
    Processing sheet with id=AB4, first strand: chain 'B' and resid 770 through 771
    Processing sheet with id=AB5, first strand: chain 'B' and resid 775 through 777
    Processing sheet with id=AB6, first strand: chain 'B' and resid 763 through 764
      removed outlier: 5.778A  pdb=" N   VAL B 839 " --> pdb=" O   VAL B 932 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 763 through 764
    Processing sheet with id=AB8, first strand: chain 'B' and resid 829 through 834
      removed outlier: 3.690A  pdb=" N   VAL B 850 " --> pdb=" O   ASP B 832 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 829 through 834
      removed outlier: 3.690A  pdb=" N   VAL B 850 " --> pdb=" O   ASP B 832 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 936 through 947
      removed outlier: 6.248A  pdb=" N   ARG B 937 " --> pdb=" O   ALA B1350 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   ALA B1350 " --> pdb=" O   ARG B 937 " (cutoff:3.500A)
      removed outlier: 5.531A  pdb=" N   ASN B 939 " --> pdb=" O   TYR B1348 " (cutoff:3.500A)
      removed outlier: 7.740A  pdb=" N   TYR B1348 " --> pdb=" O   ASN B 939 " (cutoff:3.500A)
      removed outlier: 5.584A  pdb=" N   THR B 941 " --> pdb=" O   THR B1346 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   THR B1346 " --> pdb=" O   THR B 941 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'B' and resid 959 through 962
    Processing sheet with id=AC3, first strand: chain 'B' and resid 1362 through 1368
    Processing sheet with id=AC4, first strand: chain 'B' and resid 1427 through 1428
      removed outlier: 3.543A  pdb=" N   TYR B1447 " --> pdb=" O   TYR B1428 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   ALA B1481 " --> pdb=" O   GLU B1487 " (cutoff:3.500A)
      removed outlier: 7.187A  pdb=" N   GLU B1487 " --> pdb=" O   ALA B1481 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'B' and resid 1504 through 1507
    Processing sheet with id=AC6, first strand: chain 'B' and resid 1568 through 1570
      removed outlier: 5.604A  pdb=" N   THR B1568 " --> pdb=" O   LYS B1546 " (cutoff:3.500A)
      removed outlier: 7.163A  pdb=" N   LYS B1546 " --> pdb=" O   THR B1568 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   VAL B1544 " --> pdb=" O   LYS B1570 " (cutoff:3.500A)
      removed outlier: 4.624A  pdb=" N   TYR B1543 " --> pdb=" O   GLY B1606 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   GLY B1606 " --> pdb=" O   TYR B1543 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'B' and resid 1551 through 1553
      removed outlier: 4.256A  pdb=" N   LYS B1551 " --> pdb=" O   ILE B1562 " (cutoff:3.500A)

    620 hydrogen bonds defined for protein.
    1695 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.92

  Time building geometry restraints manager: 1.24 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 2516
        1.33 -     1.45: 3315
        1.45 -     1.57: 7983
        1.57 -     1.69: 0
        1.69 -     1.81: 90
  Bond restraints: 13904
  Sorted by residual:
  bond pdb=" N   ILE C 309 "
       pdb=" CA  ILE C 309 "
    ideal  model  delta    sigma   weight residual
    1.461  1.496 -0.035 1.19e-02 7.06e+03 8.82e+00
  bond pdb=" N   GLN C 301 "
       pdb=" CA  GLN C 301 "
    ideal  model  delta    sigma   weight residual
    1.455  1.487 -0.032 1.09e-02 8.42e+03 8.37e+00
  bond pdb=" N   LYS C 303 "
       pdb=" CA  LYS C 303 "
    ideal  model  delta    sigma   weight residual
    1.454  1.488 -0.034 1.21e-02 6.83e+03 7.91e+00
  bond pdb=" N   GLU B1614 "
       pdb=" CA  GLU B1614 "
    ideal  model  delta    sigma   weight residual
    1.453  1.487 -0.034 1.22e-02 6.72e+03 7.74e+00
  bond pdb=" N   VAL C 308 "
       pdb=" CA  VAL C 308 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.25e-02 6.40e+03 7.50e+00
  ... (remaining 13899 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.13: 18362
        1.13 -     2.27: 318
        2.27 -     3.40: 107
        3.40 -     4.54: 36
        4.54 -     5.67: 9
  Bond angle restraints: 18832
  Sorted by residual:
  angle pdb=" N   LYS C 298 "
        pdb=" CA  LYS C 298 "
        pdb=" C   LYS C 298 "
      ideal   model   delta    sigma   weight residual
     111.40  105.89    5.51 1.22e+00 6.72e-01 2.04e+01
  angle pdb=" N   VAL C 299 "
        pdb=" CA  VAL C 299 "
        pdb=" C   VAL C 299 "
      ideal   model   delta    sigma   weight residual
     112.04  106.45    5.59 1.40e+00 5.10e-01 1.60e+01
  angle pdb=" CA  VAL C 295 "
        pdb=" C   VAL C 295 "
        pdb=" O   VAL C 295 "
      ideal   model   delta    sigma   weight residual
     120.64  116.49    4.15 1.09e+00 8.42e-01 1.45e+01
  angle pdb=" CA  LEU C 305 "
        pdb=" C   LEU C 305 "
        pdb=" O   LEU C 305 "
      ideal   model   delta    sigma   weight residual
     120.92  116.69    4.23 1.12e+00 7.97e-01 1.43e+01
  angle pdb=" N   PRO C 304 "
        pdb=" CA  PRO C 304 "
        pdb=" C   PRO C 304 "
      ideal   model   delta    sigma   weight residual
     111.57  117.24   -5.67 1.52e+00 4.33e-01 1.39e+01
  ... (remaining 18827 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.53: 7633
       17.53 -    35.06: 694
       35.06 -    52.58: 132
       52.58 -    70.11: 22
       70.11 -    87.64: 14
  Dihedral angle restraints: 8495
    sinusoidal: 3470
      harmonic: 5025
  Sorted by residual:
  dihedral pdb=" CB  CYS B1389 "
           pdb=" SG  CYS B1389 "
           pdb=" SG  CYS B1458 "
           pdb=" CB  CYS B1458 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -27.81  -58.19     1      1.00e+01 1.00e-02 4.54e+01
  dihedral pdb=" CB  CYS B 873 "
           pdb=" SG  CYS B 873 "
           pdb=" SG  CYS B1513 "
           pdb=" CB  CYS B1513 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   57.80   35.20     1      1.00e+01 1.00e-02 1.76e+01
  dihedral pdb=" CA  CYS B1101 "
           pdb=" CB  CYS B1101 "
           pdb=" SG  CYS B1101 "
           pdb=" SG  CYS B1158 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -73.00   -0.84  -72.16     1      2.00e+01 2.50e-03 1.66e+01
  ... (remaining 8492 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1436
       0.032 -    0.064: 417
       0.064 -    0.096: 106
       0.096 -    0.128: 156
       0.128 -    0.160: 12
  Chirality restraints: 2127
  Sorted by residual:
  chirality pdb=" CA  VAL C 299 "
            pdb=" N   VAL C 299 "
            pdb=" C   VAL C 299 "
            pdb=" CB  VAL C 299 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.37e-01
  chirality pdb=" CA  LEU B1618 "
            pdb=" N   LEU B1618 "
            pdb=" C   LEU B1618 "
            pdb=" CB  LEU B1618 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.17e-01
  chirality pdb=" CA  ILE C 309 "
            pdb=" N   ILE C 309 "
            pdb=" C   ILE C 309 "
            pdb=" CB  ILE C 309 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.04e-01
  ... (remaining 2124 not shown)

  Planarity restraints: 2429
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS C 303 "    0.012 2.00e-02 2.50e+03   2.41e-02 5.83e+00
        pdb=" C   LYS C 303 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   LYS C 303 "    0.015 2.00e-02 2.50e+03
        pdb=" N   PRO C 304 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C 223 "    0.016 2.00e-02 2.50e+03   1.49e-02 5.53e+00
        pdb=" CG  TRP C 223 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD1 TRP C 223 "    0.015 2.00e-02 2.50e+03
        pdb=" CD2 TRP C 223 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP C 223 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP C 223 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP C 223 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C 223 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C 223 "    0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP C 223 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B1173 "    0.008 2.00e-02 2.50e+03   1.61e-02 2.61e+00
        pdb=" C   GLY B1173 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   GLY B1173 "    0.010 2.00e-02 2.50e+03
        pdb=" N   ASP B1174 "    0.009 2.00e-02 2.50e+03
  ... (remaining 2426 not shown)

  Histogram of nonbonded interaction distances:
        0.88 -     1.69: 5
        1.69 -     2.49: 66
        2.49 -     3.29: 14636
        3.29 -     4.10: 31615
        4.10 -     4.90: 56736
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 103058
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B1170 "
            pdb=" OH  TYR C  70 "
     model   vdw
     0.883 3.040
  nonbonded pdb=" OE1 GLN B1112 "
            pdb=" CD  ARG C  77 "
     model   vdw
     1.071 3.440
  nonbonded pdb=" OE1 GLN B1112 "
            pdb=" NE  ARG C  77 "
     model   vdw
     1.247 3.120
  nonbonded pdb=" CE  LYS B1171 "
            pdb=" CE2 TYR C  70 "
     model   vdw
     1.250 2.992
  nonbonded pdb=" CD  GLN B1112 "
            pdb=" CZ  ARG C  77 "
     model   vdw
     1.657 2.800
  ... (remaining 103053 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
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     12.290
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5481
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      :  0.009   0.976  13915  Z= 0.920
  Angle     :  0.450   5.669  18850  Z= 0.255
  Chirality :  0.043   0.160   2127
  Planarity :  0.003   0.038   2429
  Dihedral  : 13.815  87.641   5222
  Min Nonbonded Distance : 0.883

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  2.23 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  :  0.27 %
    Favored  : 99.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.65 (0.21), residues: 1705
  helix:  2.99 (0.27), residues: 404
  sheet:  1.44 (0.23), residues: 514
  loop : -0.16 (0.23), residues: 787

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 304 
 TYR   0.013   0.001   TYR A 261 
 PHE   0.008   0.001   PHE A 112 
 TRP   0.041   0.001   TRP C 223 
 HIS   0.003   0.000   HIS A  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 (13904)
  covalent geometry    : angle       0.44962 (18832)
  SS BOND              : bond        0.00127 (    9)
  SS BOND              : angle       0.49054 (   18)
  hydrogen bonds       : bond        0.13682 (  603)
  hydrogen bonds       : angle       5.28998 ( 1695)
  Misc. bond           : bond        0.75861 (    2)

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

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

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 104
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B 1615 LYS cc_start: 0.5151 (OUTLIER) cc_final: 0.4313 (mmmt)
REVERT: B 1656 MET cc_start: -0.3946 (ptt) cc_final: -0.4661 (ptt)
  outliers start: 7
  outliers final: 0
  residues processed: 109
  average time/residue: 0.1362
  time to fit residues: 20.8862
Evaluate side-chains
  62 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 61
  time to evaluate  : 0.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 1615 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    7.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    0.0370
   chunk 130 optimal weight:    7.9990
   chunk 124 optimal weight:    0.0060
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:    7.9990
   chunk 149 optimal weight:   20.0000
   overall best weight:    2.0080

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

Flipped N/Q/H residues before XYZ refinement:
A 512 GLN
B1289 HIS
B1617 ASN
C  66 ASN
C 301 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.064905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.045878 restraints weight = 103685.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.047103 restraints weight = 52279.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.047875 restraints weight = 34637.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.048489 restraints weight = 27107.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.048588 restraints weight = 23108.532|
|-----------------------------------------------------------------------------|
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.2081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  13915  Z= 0.171
  Angle     :  0.580   7.060  18850  Z= 0.300
  Chirality :  0.043   0.222   2127
  Planarity :  0.004   0.036   2429
  Dihedral  :  3.630  57.745   1855
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.52 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  :  6.10 %
    Favored  : 93.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.42 (0.21), residues: 1705
  helix:  2.39 (0.26), residues: 423
  sheet:  1.37 (0.23), residues: 517
  loop : -0.16 (0.23), residues: 765

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 269 
 TYR   0.017   0.001   TYR C  70 
 PHE   0.017   0.002   PHE A 112 
 TRP   0.015   0.001   TRP A 552 
 HIS   0.007   0.001   HIS A 457 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 (13904)
  covalent geometry    : angle       0.57757 (18832)
  SS BOND              : bond        0.00241 (    9)
  SS BOND              : angle       1.83949 (   18)
  hydrogen bonds       : bond        0.03405 (  603)
  hydrogen bonds       : angle       4.37703 ( 1695)
  Misc. bond           : bond        0.00331 (    2)

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

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

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 70
  time to evaluate  : 0.507 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B 1129 MET cc_start: 0.8927 (mmm) cc_final: 0.8524 (mmm)
REVERT: B 1141 MET cc_start: 0.8931 (mmm) cc_final: 0.8413 (mmm)
REVERT: B 1407 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.7343 (ptp)
REVERT: B 1656 MET cc_start: -0.3019 (ptt) cc_final: -0.3444 (ptt)
  outliers start: 11
  outliers final: 5
  residues processed: 76
  average time/residue: 0.1088
  time to fit residues: 12.7378
Evaluate side-chains
  65 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 59
  time to evaluate  : 0.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain B residue  862 VAL
Chi-restraints excluded: chain B residue 1407 MET
Chi-restraints excluded: chain C residue   66 ASN
Chi-restraints excluded: chain C residue  212 SER
Chi-restraints excluded: chain C residue  288 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 75 optimal weight:    0.6980
   chunk 139 optimal weight:    9.9990
   chunk 77 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 37 optimal weight:    9.9990
   chunk 46 optimal weight:    5.9990
   chunk 4 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 115 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9980
   chunk 126 optimal weight:    9.9990
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
A 216 GLN
A 589 HIS
B1198 GLN
C 282 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.064011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.044840 restraints weight = 104429.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.046059 restraints weight = 51959.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.046825 restraints weight = 34503.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.047450 restraints weight = 26920.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.047558 restraints weight = 22812.638|
|-----------------------------------------------------------------------------|
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.2783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  13915  Z= 0.167
  Angle     :  0.539   8.508  18850  Z= 0.279
  Chirality :  0.042   0.160   2127
  Planarity :  0.003   0.048   2429
  Dihedral  :  3.458  17.447   1851
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.52 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  :  7.82 %
    Favored  : 91.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.33 (0.21), residues: 1705
  helix:  2.36 (0.26), residues: 428
  sheet:  1.35 (0.23), residues: 530
  loop : -0.35 (0.23), residues: 747

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 481 
 TYR   0.016   0.001   TYR B1194 
 PHE   0.015   0.001   PHE A 112 
 TRP   0.013   0.001   TRP B1255 
 HIS   0.007   0.001   HIS A  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 (13904)
  covalent geometry    : angle       0.53615 (18832)
  SS BOND              : bond        0.00219 (    9)
  SS BOND              : angle       1.98209 (   18)
  hydrogen bonds       : bond        0.03120 (  603)
  hydrogen bonds       : angle       4.31095 ( 1695)
  Misc. bond           : bond        0.00102 (    2)

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

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

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 63
  time to evaluate  : 0.587 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.8223 (tmm)
REVERT: B 1015 MET cc_start: 0.8822 (mmp) cc_final: 0.8616 (mmp)
REVERT: B 1129 MET cc_start: 0.9141 (mmm) cc_final: 0.8618 (mmm)
REVERT: B 1141 MET cc_start: 0.9262 (mmm) cc_final: 0.8851 (mmm)
REVERT: B 1407 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.7733 (ptp)
REVERT: B 1563 MET cc_start: -0.1561 (tmm) cc_final: -0.1772 (tmm)
REVERT: B 1656 MET cc_start: -0.3116 (ptt) cc_final: -0.3516 (ptt)
REVERT: C   66 ASN cc_start: 0.9014 (OUTLIER) cc_final: 0.8649 (p0)
  outliers start: 15
  outliers final: 5
  residues processed: 74
  average time/residue: 0.1085
  time to fit residues: 12.4606
Evaluate side-chains
  66 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.709 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue  338 MET
Chi-restraints excluded: chain B residue  862 VAL
Chi-restraints excluded: chain B residue 1199 MET
Chi-restraints excluded: chain B residue 1202 LEU
Chi-restraints excluded: chain B residue 1407 MET
Chi-restraints excluded: chain B residue 1408 MET
Chi-restraints excluded: chain C residue   66 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 107 optimal weight:    8.9990
   chunk 117 optimal weight:    5.9990
   chunk 160 optimal weight:   20.0000
   chunk 66 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 104 optimal weight:    0.9980
   chunk 3 optimal weight:   10.0000
   chunk 80 optimal weight:    6.9990
   chunk 64 optimal weight:    3.9990
   chunk 36 optimal weight:    9.9990
   overall best weight:    3.1988

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

Flipped N/Q/H residues before XYZ refinement:
A  47 HIS
A 126 GLN
B1270 GLN
B1355 GLN
C  66 ASN
** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.062315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.042814 restraints weight = 105127.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.044014 restraints weight = 52233.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.044761 restraints weight = 34899.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.045338 restraints weight = 27391.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.045518 restraints weight = 23374.206|
|-----------------------------------------------------------------------------|
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.3771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  13915  Z= 0.235
  Angle     :  0.626  11.364  18850  Z= 0.318
  Chirality :  0.043   0.163   2127
  Planarity :  0.004   0.046   2429
  Dihedral  :  3.988  20.210   1851
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.28 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  :  9.22 %
    Favored  : 89.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.01 (0.21), residues: 1705
  helix:  2.11 (0.26), residues: 430
  sheet:  1.10 (0.23), residues: 527
  loop : -0.51 (0.23), residues: 748

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  91 
 TYR   0.026   0.002   TYR C  70 
 PHE   0.022   0.002   PHE A 112 
 TRP   0.016   0.002   TRP B1255 
 HIS   0.010   0.002   HIS A  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00507 (13904)
  covalent geometry    : angle       0.62196 (18832)
  SS BOND              : bond        0.00266 (    9)
  SS BOND              : angle       2.51264 (   18)
  hydrogen bonds       : bond        0.03373 (  603)
  hydrogen bonds       : angle       4.58960 ( 1695)
  Misc. bond           : bond        0.00192 (    2)

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

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

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 66
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.8326 (tmm)
REVERT: B 1129 MET cc_start: 0.9199 (mmm) cc_final: 0.8864 (mmm)
REVERT: B 1141 MET cc_start: 0.9463 (mmm) cc_final: 0.9008 (mmm)
REVERT: B 1407 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.7883 (ptp)
REVERT: B 1656 MET cc_start: -0.2913 (ptt) cc_final: -0.3699 (ptt)
REVERT: C   45 MET cc_start: 0.8548 (mmm) cc_final: 0.8203 (mmm)
REVERT: C   66 ASN cc_start: 0.8346 (OUTLIER) cc_final: 0.8097 (p0)
REVERT: C  265 VAL cc_start: 0.9188 (OUTLIER) cc_final: 0.8874 (m)
  outliers start: 19
  outliers final: 9
  residues processed: 80
  average time/residue: 0.0991
  time to fit residues: 12.5369
Evaluate side-chains
  73 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 60
  time to evaluate  : 0.552 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue  338 MET
Chi-restraints excluded: chain B residue  862 VAL
Chi-restraints excluded: chain B residue 1078 LEU
Chi-restraints excluded: chain B residue 1177 GLU
Chi-restraints excluded: chain B residue 1202 LEU
Chi-restraints excluded: chain B residue 1407 MET
Chi-restraints excluded: chain B residue 1408 MET
Chi-restraints excluded: chain C residue   66 ASN
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  265 VAL
Chi-restraints excluded: chain C residue  288 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 102 optimal weight:    3.9990
   chunk 81 optimal weight:    6.9990
   chunk 51 optimal weight:    7.9990
   chunk 91 optimal weight:    5.9990
   chunk 88 optimal weight:    7.9990
   chunk 27 optimal weight:    1.9990
   chunk 93 optimal weight:    6.9990
   chunk 87 optimal weight:    2.9990
   chunk 9 optimal weight:    4.9990
   chunk 109 optimal weight:    0.3980
   chunk 36 optimal weight:    0.0670
   overall best weight:    1.8924

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

Flipped N/Q/H residues before XYZ refinement:
C  66 ASN
** C 217 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 = 0.3697 r_free = 0.3697 target = 0.062575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.042980 restraints weight = 102239.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.044179 restraints weight = 50244.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.044912 restraints weight = 33223.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.045468 restraints weight = 26273.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.045674 restraints weight = 22362.152|
|-----------------------------------------------------------------------------|
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.3839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13915  Z= 0.152
  Angle     :  0.550   8.782  18850  Z= 0.280
  Chirality :  0.043   0.153   2127
  Planarity :  0.003   0.043   2429
  Dihedral  :  3.808  17.798   1851
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.76 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 10.48 %
    Favored  : 88.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.08 (0.21), residues: 1705
  helix:  2.20 (0.26), residues: 431
  sheet:  1.20 (0.23), residues: 519
  loop : -0.51 (0.23), residues: 755

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 269 
 TYR   0.042   0.001   TYR C  70 
 PHE   0.014   0.001   PHE A 112 
 TRP   0.017   0.001   TRP C 223 
 HIS   0.004   0.001   HIS A 333 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 (13904)
  covalent geometry    : angle       0.54477 (18832)
  SS BOND              : bond        0.00153 (    9)
  SS BOND              : angle       2.41370 (   18)
  hydrogen bonds       : bond        0.03087 (  603)
  hydrogen bonds       : angle       4.43355 ( 1695)
  Misc. bond           : bond        0.00235 (    2)

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

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

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 62
  time to evaluate  : 0.544 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.8235 (tmm)
REVERT: A  368 MET cc_start: 0.8467 (mmm) cc_final: 0.8169 (ttt)
REVERT: B 1129 MET cc_start: 0.9169 (mmm) cc_final: 0.8829 (mmm)
REVERT: B 1141 MET cc_start: 0.9449 (mmm) cc_final: 0.9003 (mmm)
REVERT: B 1407 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.7657 (ptm)
REVERT: B 1656 MET cc_start: -0.2711 (ptt) cc_final: -0.3502 (ptt)
REVERT: C   45 MET cc_start: 0.8727 (mmm) cc_final: 0.8305 (mmm)
REVERT: C  217 GLN cc_start: 0.8433 (mm-40) cc_final: 0.8079 (mm-40)
  outliers start: 17
  outliers final: 10
  residues processed: 75
  average time/residue: 0.1061
  time to fit residues: 12.4189
Evaluate side-chains
  72 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 60
  time to evaluate  : 0.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue  338 MET
Chi-restraints excluded: chain B residue  829 PHE
Chi-restraints excluded: chain B residue  862 VAL
Chi-restraints excluded: chain B residue  944 VAL
Chi-restraints excluded: chain B residue 1177 GLU
Chi-restraints excluded: chain B residue 1202 LEU
Chi-restraints excluded: chain B residue 1407 MET
Chi-restraints excluded: chain B residue 1408 MET
Chi-restraints excluded: chain B residue 1511 CYS
Chi-restraints excluded: chain C residue  288 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 154 optimal weight:    5.9990
   chunk 159 optimal weight:    6.9990
   chunk 109 optimal weight:    3.9990
   chunk 150 optimal weight:   10.0000
   chunk 65 optimal weight:    3.9990
   chunk 112 optimal weight:    9.9990
   chunk 5 optimal weight:    0.9980
   chunk 124 optimal weight:    0.3980
   chunk 104 optimal weight:   10.0000
   chunk 22 optimal weight:    6.9990
   chunk 96 optimal weight:    7.9990
   overall best weight:    3.0786

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

Flipped N/Q/H residues before XYZ refinement:
B1349 HIS
C  66 ASN
C 120 GLN
** C 217 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 = 0.3671 r_free = 0.3671 target = 0.061620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.042143 restraints weight = 105262.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.043312 restraints weight = 52441.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.044098 restraints weight = 34996.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.044599 restraints weight = 27415.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.044722 restraints weight = 23568.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.4311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  13915  Z= 0.227
  Angle     :  0.603   9.643  18850  Z= 0.308
  Chirality :  0.043   0.147   2127
  Planarity :  0.004   0.044   2429
  Dihedral  :  4.037  19.006   1851
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.58 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 10.61 %
    Favored  : 87.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.97 (0.21), residues: 1705
  helix:  2.16 (0.26), residues: 421
  sheet:  1.01 (0.23), residues: 533
  loop : -0.50 (0.23), residues: 751

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  91 
 TYR   0.055   0.002   TYR C  70 
 PHE   0.017   0.002   PHE A 112 
 TRP   0.024   0.002   TRP C 223 
 HIS   0.005   0.001   HIS C 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00489 (13904)
  covalent geometry    : angle       0.59790 (18832)
  SS BOND              : bond        0.00244 (    9)
  SS BOND              : angle       2.60041 (   18)
  hydrogen bonds       : bond        0.03305 (  603)
  hydrogen bonds       : angle       4.58141 ( 1695)
  Misc. bond           : bond        0.00294 (    2)

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

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

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 62
  time to evaluate  : 0.554 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.8307 (tmm)
REVERT: B 1015 MET cc_start: 0.9007 (mmp) cc_final: 0.8700 (mmp)
REVERT: B 1018 MET cc_start: 0.8677 (ptm) cc_final: 0.8341 (ptp)
REVERT: B 1129 MET cc_start: 0.9198 (mmm) cc_final: 0.8844 (mmm)
REVERT: B 1141 MET cc_start: 0.9505 (mmm) cc_final: 0.9104 (mmm)
REVERT: B 1347 MET cc_start: 0.7664 (mmm) cc_final: 0.7232 (mmm)
REVERT: B 1407 MET cc_start: 0.8544 (mtm) cc_final: 0.7763 (ptm)
REVERT: B 1656 MET cc_start: -0.2422 (ptt) cc_final: -0.3216 (ptt)
REVERT: C  217 GLN cc_start: 0.8538 (mm-40) cc_final: 0.8320 (mm-40)
  outliers start: 23
  outliers final: 19
  residues processed: 81
  average time/residue: 0.1012
  time to fit residues: 13.1386
Evaluate side-chains
  78 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 58
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue  338 MET
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  430 GLU
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain B residue  829 PHE
Chi-restraints excluded: chain B residue  862 VAL
Chi-restraints excluded: chain B residue  944 VAL
Chi-restraints excluded: chain B residue 1078 LEU
Chi-restraints excluded: chain B residue 1177 GLU
Chi-restraints excluded: chain B residue 1202 LEU
Chi-restraints excluded: chain B residue 1216 ASP
Chi-restraints excluded: chain B residue 1408 MET
Chi-restraints excluded: chain B residue 1511 CYS
Chi-restraints excluded: chain C residue   66 ASN
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  265 VAL
Chi-restraints excluded: chain C residue  288 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 105 optimal weight:   10.0000
   chunk 76 optimal weight:    0.0060
   chunk 6 optimal weight:    6.9990
   chunk 30 optimal weight:    7.9990
   chunk 69 optimal weight:    0.9980
   chunk 103 optimal weight:    0.6980
   chunk 91 optimal weight:    9.9990
   chunk 74 optimal weight:    3.9990
   chunk 24 optimal weight:    5.9990
   chunk 70 optimal weight:    3.9990
   chunk 106 optimal weight:    0.6980
   overall best weight:    1.2798

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

Flipped N/Q/H residues before XYZ refinement:
** B 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  66 ASN
** C 217 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 = 0.3699 r_free = 0.3699 target = 0.062542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.043062 restraints weight = 104296.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.044241 restraints weight = 51413.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.045084 restraints weight = 34379.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.045386 restraints weight = 26741.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.045819 restraints weight = 23664.541|
|-----------------------------------------------------------------------------|
r_work (final): 0.3033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.4289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  13915  Z= 0.122
  Angle     :  0.555  10.285  18850  Z= 0.278
  Chirality :  0.043   0.151   2127
  Planarity :  0.003   0.039   2429
  Dihedral  :  3.790  17.657   1851
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.87 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 11.54 %
    Favored  : 87.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.00 (0.21), residues: 1705
  helix:  2.12 (0.26), residues: 427
  sheet:  1.11 (0.23), residues: 520
  loop : -0.51 (0.23), residues: 758

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  91 
 TYR   0.039   0.001   TYR C  70 
 PHE   0.010   0.001   PHE A 112 
 TRP   0.022   0.001   TRP C 223 
 HIS   0.006   0.001   HIS C 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 (13904)
  covalent geometry    : angle       0.55077 (18832)
  SS BOND              : bond        0.00196 (    9)
  SS BOND              : angle       2.19149 (   18)
  hydrogen bonds       : bond        0.02958 (  603)
  hydrogen bonds       : angle       4.38859 ( 1695)
  Misc. bond           : bond        0.00159 (    2)

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

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

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 62
  time to evaluate  : 0.478 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 MET cc_start: 0.8942 (ptp) cc_final: 0.8339 (pmm)
REVERT: A  338 MET cc_start: 0.9101 (OUTLIER) cc_final: 0.8271 (tmm)
REVERT: B 1015 MET cc_start: 0.9098 (mmp) cc_final: 0.8860 (mmp)
REVERT: B 1129 MET cc_start: 0.9150 (mmm) cc_final: 0.8790 (mmm)
REVERT: B 1141 MET cc_start: 0.9501 (mmm) cc_final: 0.9078 (mmm)
REVERT: B 1202 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8797 (tt)
REVERT: B 1407 MET cc_start: 0.8489 (mtm) cc_final: 0.7686 (ptm)
REVERT: B 1656 MET cc_start: -0.2804 (ptt) cc_final: -0.3594 (ptt)
REVERT: C   45 MET cc_start: 0.8027 (mmm) cc_final: 0.7791 (mmm)
  outliers start: 21
  outliers final: 11
  residues processed: 79
  average time/residue: 0.0944
  time to fit residues: 12.1752
Evaluate side-chains
  72 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 59
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue  338 MET
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  554 ASP
Chi-restraints excluded: chain B residue 1177 GLU
Chi-restraints excluded: chain B residue 1202 LEU
Chi-restraints excluded: chain B residue 1408 MET
Chi-restraints excluded: chain B residue 1511 CYS
Chi-restraints excluded: chain C residue   66 ASN
Chi-restraints excluded: chain C residue  265 VAL
Chi-restraints excluded: chain C residue  288 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 114 optimal weight:   10.0000
   chunk 6 optimal weight:    3.9990
   chunk 65 optimal weight:    4.9990
   chunk 96 optimal weight:    7.9990
   chunk 164 optimal weight:    0.7980
   chunk 108 optimal weight:    9.9990
   chunk 20 optimal weight:    2.9990
   chunk 134 optimal weight:    2.9990
   chunk 101 optimal weight:    9.9990
   chunk 106 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
** B 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  66 ASN
** C 217 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 = 0.3683 r_free = 0.3683 target = 0.062047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.042608 restraints weight = 104317.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.043783 restraints weight = 51925.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.044571 restraints weight = 34756.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.045002 restraints weight = 27301.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.045108 restraints weight = 23748.860|
|-----------------------------------------------------------------------------|
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.4470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  13915  Z= 0.177
  Angle     :  0.597  13.700  18850  Z= 0.296
  Chirality :  0.043   0.167   2127
  Planarity :  0.004   0.040   2429
  Dihedral  :  3.891  19.046   1851
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.64 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 11.80 %
    Favored  : 86.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.88 (0.21), residues: 1705
  helix:  2.05 (0.26), residues: 427
  sheet:  0.96 (0.23), residues: 526
  loop : -0.54 (0.23), residues: 752

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  91 
 TYR   0.060   0.001   TYR C  70 
 PHE   0.011   0.001   PHE A 112 
 TRP   0.027   0.002   TRP C 223 
 HIS   0.006   0.001   HIS C 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 (13904)
  covalent geometry    : angle       0.59271 (18832)
  SS BOND              : bond        0.00189 (    9)
  SS BOND              : angle       2.34592 (   18)
  hydrogen bonds       : bond        0.03126 (  603)
  hydrogen bonds       : angle       4.50115 ( 1695)
  Misc. bond           : bond        0.00246 (    2)

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

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

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 57
  time to evaluate  : 0.540 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 MET cc_start: 0.8929 (ptp) cc_final: 0.8364 (pmm)
REVERT: A  338 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8314 (tmm)
REVERT: B 1015 MET cc_start: 0.9092 (mmp) cc_final: 0.8738 (mmp)
REVERT: B 1018 MET cc_start: 0.8563 (ptm) cc_final: 0.8270 (ptp)
REVERT: B 1129 MET cc_start: 0.9174 (mmm) cc_final: 0.8804 (mmm)
REVERT: B 1141 MET cc_start: 0.9499 (mmm) cc_final: 0.9136 (mmm)
REVERT: B 1202 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8793 (tt)
REVERT: B 1407 MET cc_start: 0.8514 (mtm) cc_final: 0.8014 (ptp)
REVERT: B 1548 ARG cc_start: 0.9401 (OUTLIER) cc_final: 0.9174 (ttp80)
REVERT: B 1656 MET cc_start: -0.2710 (ptt) cc_final: -0.3334 (ptt)
REVERT: C   45 MET cc_start: 0.8155 (mmm) cc_final: 0.7893 (mmm)
  outliers start: 20
  outliers final: 15
  residues processed: 74
  average time/residue: 0.1169
  time to fit residues: 13.5506
Evaluate side-chains
  74 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 56
  time to evaluate  : 0.599 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue  338 MET
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  430 GLU
Chi-restraints excluded: chain B residue  829 PHE
Chi-restraints excluded: chain B residue  862 VAL
Chi-restraints excluded: chain B residue 1133 LEU
Chi-restraints excluded: chain B residue 1177 GLU
Chi-restraints excluded: chain B residue 1202 LEU
Chi-restraints excluded: chain B residue 1408 MET
Chi-restraints excluded: chain B residue 1511 CYS
Chi-restraints excluded: chain B residue 1548 ARG
Chi-restraints excluded: chain C residue   66 ASN
Chi-restraints excluded: chain C residue   70 TYR
Chi-restraints excluded: chain C residue  265 VAL
Chi-restraints excluded: chain C residue  288 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 76 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9990
   chunk 129 optimal weight:    0.0770
   chunk 94 optimal weight:    6.9990
   chunk 102 optimal weight:    4.9990
   chunk 93 optimal weight:    0.9980
   chunk 133 optimal weight:    2.9990
   chunk 158 optimal weight:    0.0980
   chunk 52 optimal weight:    5.9990
   chunk 143 optimal weight:    8.9990
   overall best weight:    1.0342

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

Flipped N/Q/H residues before XYZ refinement:
** B 868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 989 GLN
C  66 ASN
** C 217 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 = 0.3701 r_free = 0.3701 target = 0.062598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.043158 restraints weight = 101006.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.044373 restraints weight = 49538.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.045152 restraints weight = 32662.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.045707 restraints weight = 25442.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.045881 restraints weight = 21559.368|
|-----------------------------------------------------------------------------|
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.4412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  13915  Z= 0.111
  Angle     :  0.577  13.517  18850  Z= 0.283
  Chirality :  0.043   0.174   2127
  Planarity :  0.003   0.040   2429
  Dihedral  :  3.714  17.544   1851
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.99 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 12.40 %
    Favored  : 86.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.92 (0.21), residues: 1705
  helix:  2.07 (0.26), residues: 427
  sheet:  1.02 (0.23), residues: 520
  loop : -0.52 (0.23), residues: 758

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C  91 
 TYR   0.049   0.001   TYR C  70 
 PHE   0.009   0.001   PHE A 529 
 TRP   0.030   0.001   TRP C 223 
 HIS   0.006   0.001   HIS C 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 (13904)
  covalent geometry    : angle       0.57436 (18832)
  SS BOND              : bond        0.00177 (    9)
  SS BOND              : angle       2.01828 (   18)
  hydrogen bonds       : bond        0.02878 (  603)
  hydrogen bonds       : angle       4.37229 ( 1695)
  Misc. bond           : bond        0.00163 (    2)

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

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

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 57
  time to evaluate  : 0.561 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 MET cc_start: 0.8897 (ptp) cc_final: 0.8322 (pmm)
REVERT: A  338 MET cc_start: 0.9118 (OUTLIER) cc_final: 0.8291 (tmm)
REVERT: B 1015 MET cc_start: 0.9130 (mmp) cc_final: 0.8761 (mmp)
REVERT: B 1018 MET cc_start: 0.8540 (ptm) cc_final: 0.8231 (ptp)
REVERT: B 1129 MET cc_start: 0.9131 (mmm) cc_final: 0.8752 (mmm)
REVERT: B 1141 MET cc_start: 0.9486 (mmm) cc_final: 0.9088 (mmm)
REVERT: B 1407 MET cc_start: 0.8482 (mtm) cc_final: 0.7979 (ptp)
REVERT: B 1548 ARG cc_start: 0.9411 (OUTLIER) cc_final: 0.9172 (ttp80)
REVERT: B 1656 MET cc_start: -0.2790 (ptt) cc_final: -0.3404 (ptt)
REVERT: C   45 MET cc_start: 0.8209 (mmm) cc_final: 0.7953 (mmm)
  outliers start: 17
  outliers final: 10
  residues processed: 71
  average time/residue: 0.0949
  time to fit residues: 10.8797
Evaluate side-chains
  68 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 56
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue  338 MET
Chi-restraints excluded: chain B residue 1177 GLU
Chi-restraints excluded: chain B residue 1202 LEU
Chi-restraints excluded: chain B residue 1408 MET
Chi-restraints excluded: chain B residue 1511 CYS
Chi-restraints excluded: chain B residue 1548 ARG
Chi-restraints excluded: chain C residue   66 ASN
Chi-restraints excluded: chain C residue   70 TYR
Chi-restraints excluded: chain C residue  265 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 88 optimal weight:    0.7980
   chunk 78 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 37 optimal weight:    9.9990
   chunk 56 optimal weight:    4.9990
   chunk 115 optimal weight:    1.9990
   chunk 152 optimal weight:   30.0000
   chunk 35 optimal weight:    0.0170
   chunk 154 optimal weight:    6.9990
   chunk 3 optimal weight:    9.9990
   chunk 165 optimal weight:    6.9990
   overall best weight:    1.3624

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

Flipped N/Q/H residues before XYZ refinement:
** B 868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  66 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.062604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.043276 restraints weight = 103961.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.044461 restraints weight = 51186.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.045309 restraints weight = 34163.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.045602 restraints weight = 26474.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.046037 restraints weight = 23453.991|
|-----------------------------------------------------------------------------|
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.4470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13915  Z= 0.123
  Angle     :  0.574  13.320  18850  Z= 0.282
  Chirality :  0.043   0.169   2127
  Planarity :  0.003   0.040   2429
  Dihedral  :  3.684  17.921   1851
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.23 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 12.20 %
    Favored  : 86.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.91 (0.21), residues: 1705
  helix:  2.03 (0.26), residues: 430
  sheet:  1.00 (0.23), residues: 523
  loop : -0.52 (0.23), residues: 752

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C  91 
 TYR   0.057   0.001   TYR C  70 
 PHE   0.014   0.001   PHE A 357 
 TRP   0.033   0.001   TRP C 223 
 HIS   0.006   0.001   HIS C 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 (13904)
  covalent geometry    : angle       0.57115 (18832)
  SS BOND              : bond        0.00187 (    9)
  SS BOND              : angle       2.02584 (   18)
  hydrogen bonds       : bond        0.02876 (  603)
  hydrogen bonds       : angle       4.36095 ( 1695)
  Misc. bond           : bond        0.00245 (    2)

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

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

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3410 Ramachandran restraints generated.
    1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 56
  time to evaluate  : 0.477 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 MET cc_start: 0.8877 (ptp) cc_final: 0.8377 (pmm)
REVERT: A  338 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8303 (tmm)
REVERT: A  373 MET cc_start: 0.8529 (mmp) cc_final: 0.7981 (mmp)
REVERT: B 1015 MET cc_start: 0.9141 (mmp) cc_final: 0.8763 (mmp)
REVERT: B 1018 MET cc_start: 0.8551 (ptm) cc_final: 0.8246 (ptp)
REVERT: B 1129 MET cc_start: 0.9150 (mmm) cc_final: 0.8771 (mmm)
REVERT: B 1141 MET cc_start: 0.9486 (mmm) cc_final: 0.9087 (mmm)
REVERT: B 1407 MET cc_start: 0.8468 (mtm) cc_final: 0.8002 (ptp)
REVERT: B 1548 ARG cc_start: 0.9405 (OUTLIER) cc_final: 0.9155 (ttp80)
REVERT: B 1656 MET cc_start: -0.2867 (ptt) cc_final: -0.3462 (ptt)
REVERT: C   45 MET cc_start: 0.8251 (mmm) cc_final: 0.8005 (mmm)
  outliers start: 18
  outliers final: 11
  residues processed: 72
  average time/residue: 0.0980
  time to fit residues: 11.4147
Evaluate side-chains
  69 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 56
  time to evaluate  : 0.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue  338 MET
Chi-restraints excluded: chain B residue  829 PHE
Chi-restraints excluded: chain B residue  862 VAL
Chi-restraints excluded: chain B residue 1177 GLU
Chi-restraints excluded: chain B residue 1202 LEU
Chi-restraints excluded: chain B residue 1408 MET
Chi-restraints excluded: chain B residue 1511 CYS
Chi-restraints excluded: chain B residue 1548 ARG
Chi-restraints excluded: chain C residue   70 TYR
Chi-restraints excluded: chain C residue  265 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 115 optimal weight:    2.9990
   chunk 2 optimal weight:    8.9990
   chunk 133 optimal weight:    5.9990
   chunk 117 optimal weight:    8.9990
   chunk 139 optimal weight:    0.0020
   chunk 166 optimal weight:    9.9990
   chunk 41 optimal weight:    0.5980
   chunk 155 optimal weight:    9.9990
   chunk 111 optimal weight:    0.7980
   chunk 124 optimal weight:    0.5980
   chunk 135 optimal weight:    4.9990
   overall best weight:    0.9990

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

Flipped N/Q/H residues before XYZ refinement:
B 868 HIS
B 989 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.062729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.043347 restraints weight = 101276.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.044524 restraints weight = 49384.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.045334 restraints weight = 32663.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.045685 restraints weight = 25237.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.046164 restraints weight = 22133.690|
|-----------------------------------------------------------------------------|
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.4466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  13915  Z= 0.106
  Angle     :  0.567  12.847  18850  Z= 0.276
  Chirality :  0.043   0.165   2127
  Planarity :  0.003   0.038   2429
  Dihedral  :  3.582  17.679   1851
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.70 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 12.40 %
    Favored  : 86.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.95 (0.21), residues: 1705
  helix:  2.07 (0.26), residues: 429
  sheet:  1.06 (0.23), residues: 521
  loop : -0.52 (0.23), residues: 755

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG C  91 
 TYR   0.052   0.001   TYR C  70 
 PHE   0.012   0.001   PHE A 357 
 TRP   0.034   0.001   TRP C 223 
 HIS   0.006   0.001   HIS C 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 (13904)
  covalent geometry    : angle       0.56448 (18832)
  SS BOND              : bond        0.00178 (    9)
  SS BOND              : angle       1.85997 (   18)
  hydrogen bonds       : bond        0.02746 (  603)
  hydrogen bonds       : angle       4.25883 ( 1695)
  Misc. bond           : bond        0.00212 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2862.88 seconds
wall clock time: 49 minutes 55.60 seconds (2995.60 seconds total)