Starting phenix.real_space_refine
on Wed May 14 03:17:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sql_40709/05_2025/8sql_40709.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sql_40709/05_2025/8sql_40709.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sql_40709/05_2025/8sql_40709.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sql_40709/05_2025/8sql_40709.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sql_40709/05_2025/8sql_40709.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sql_40709/05_2025/8sql_40709.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.142
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      51      5.16       5
     C    7271      2.51       5
     N    1871      2.21       5
     O    2023      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 97 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 11218
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 11078
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1396, 11078
          Classifications: {'peptide': 1396}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 42, 'TRANS': 1353}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 59
          Unresolved non-hydrogen angles: 74
          Unresolved non-hydrogen dihedrals: 55
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 2, 'TRP:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 26
    Chain: "B"
      Number of atoms: 65
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 65
          Classifications: {'peptide': 13}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'TRANS': 12}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 39
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'UNK:plan-1': 13}
          Unresolved non-hydrogen planarities: 13
    Chain: "A"
      Number of atoms: 75
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 75
          Unusual residues: {'PTY': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 25
  Time building chain proxies: 7.41, per 1000 atoms: 0.66
  Number of scatterers: 11218
  At special positions: 0
  Unit cell: (85.49, 108.15, 153.47, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      51     16.00
     P       2     15.00
     O    2023      8.00
     N    1871      7.00
     C    7271      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.82
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2670

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 8 sheets defined
      73.0% alpha, 8.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.49
  Creating SS restraints...
    Processing helix  chain 'A' and resid 29 through 36
    Processing helix  chain 'A' and resid 36 through 60
      removed outlier: 4.185A  pdb=" N   LYS A  60 " --> pdb=" O   LEU A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 94
      removed outlier: 3.649A  pdb=" N   VAL A  73 " --> pdb=" O   ASN A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 128
      removed outlier: 3.656A  pdb=" N   TRP A 122 " --> pdb=" O   LEU A 118 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ASP A 126 " --> pdb=" O   TRP A 122 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   ARG A 127 " --> pdb=" O   ILE A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 132 through 161
    Processing helix  chain 'A' and resid 165 through 189
    Processing helix  chain 'A' and resid 210 through 215
      removed outlier: 4.151A  pdb=" N   SER A 214 " --> pdb=" O   ASN A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 223
    Processing helix  chain 'A' and resid 226 through 236
    Processing helix  chain 'A' and resid 239 through 243
    Processing helix  chain 'A' and resid 251 through 269
      removed outlier: 3.796A  pdb=" N   ASN A 265 " --> pdb=" O   LYS A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 323
      removed outlier: 6.023A  pdb=" N   SER A 285 " --> pdb=" O   ARG A 281 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   LYS A 286 " --> pdb=" O   THR A 282 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   MET A 287 " --> pdb=" O   PHE A 283 " (cutoff:3.500A)
      Proline residue:  A 305  - end of helix
    Processing helix  chain 'A' and resid 341 through 392
      removed outlier: 3.947A  pdb=" N   GLY A 345 " --> pdb=" O   PRO A 341 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ALA A 383 " --> pdb=" O   SER A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 393 through 400
    Processing helix  chain 'A' and resid 401 through 411
    Processing helix  chain 'A' and resid 411 through 424
      removed outlier: 3.533A  pdb=" N   LEU A 416 " --> pdb=" O   ASP A 412 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   THR A 420 " --> pdb=" O   LEU A 416 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   GLN A 421 " --> pdb=" O   GLN A 417 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   TRP A 422 " --> pdb=" O   ASP A 418 " (cutoff:3.500A)
      removed outlier: 4.626A  pdb=" N   ASN A 424 " --> pdb=" O   THR A 420 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 424 through 445
      Proline residue:  A 430  - end of helix
    Processing helix  chain 'A' and resid 447 through 493
      removed outlier: 4.097A  pdb=" N   GLY A 451 " --> pdb=" O   SER A 447 " (cutoff:3.500A)
      Proline residue:  A 460  - end of helix
    Processing helix  chain 'A' and resid 493 through 500
    Processing helix  chain 'A' and resid 502 through 517
    Processing helix  chain 'A' and resid 517 through 555
      removed outlier: 3.518A  pdb=" N   LYS A 524 " --> pdb=" O   LYS A 520 " (cutoff:3.500A)
      Proline residue:  A 540  - end of helix
      removed outlier: 4.029A  pdb=" N   SER A 544 " --> pdb=" O   PRO A 540 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 560 through 603
      removed outlier: 3.909A  pdb=" N   PHE A 565 " --> pdb=" O   THR A 561 " (cutoff:3.500A)
      Proline residue:  A 566  - end of helix
      removed outlier: 3.989A  pdb=" N   PHE A 576 " --> pdb=" O   ASN A 572 " (cutoff:3.500A)
      Proline residue:  A 577  - end of helix
      Proline residue:  A 582  - end of helix
    Processing helix  chain 'A' and resid 668 through 678
      removed outlier: 3.730A  pdb=" N   LEU A 673 " --> pdb=" O   LYS A 669 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 707 through 713
    Processing helix  chain 'A' and resid 718 through 729
    Processing helix  chain 'A' and resid 730 through 738
      removed outlier: 4.472A  pdb=" N   ASP A 734 " --> pdb=" O   ALA A 730 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 740 through 743
    Processing helix  chain 'A' and resid 747 through 751
      removed outlier: 3.691A  pdb=" N   ILE A 751 " --> pdb=" O   GLU A 748 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 754 through 770
      removed outlier: 3.757A  pdb=" N   ARG A 770 " --> pdb=" O   ALA A 766 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 778 through 783
      removed outlier: 3.760A  pdb=" N   ALA A 781 " --> pdb=" O   ASP A 778 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ALA A 782 " --> pdb=" O   PRO A 779 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 784 through 795
    Processing helix  chain 'A' and resid 813 through 820
      removed outlier: 3.578A  pdb=" N   LEU A 817 " --> pdb=" O   LYS A 813 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 837 through 843
    Processing helix  chain 'A' and resid 845 through 852
    Processing helix  chain 'A' and resid 935 through 946
      removed outlier: 3.513A  pdb=" N   TYR A 939 " --> pdb=" O   LYS A 935 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 947 through 982
    Processing helix  chain 'A' and resid 987 through 1016
    Processing helix  chain 'A' and resid 1017 through 1035
    Processing helix  chain 'A' and resid 1037 through 1044
      removed outlier: 3.738A  pdb=" N   PHE A1041 " --> pdb=" O   PRO A1037 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1045 through 1055
      removed outlier: 3.643A  pdb=" N   ARG A1052 " --> pdb=" O   ARG A1048 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   PHE A1053 " --> pdb=" O   ILE A1049 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1055 through 1063
    Processing helix  chain 'A' and resid 1063 through 1089
    Processing helix  chain 'A' and resid 1092 through 1138
      Proline residue:  A1098  - end of helix
      removed outlier: 3.732A  pdb=" N   ARG A1115 " --> pdb=" O   LEU A1111 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   SER A1126 " --> pdb=" O   SER A1122 " (cutoff:3.500A)
      Proline residue:  A1127  - end of helix
    Processing helix  chain 'A' and resid 1138 through 1145
    Processing helix  chain 'A' and resid 1147 through 1201
      Proline residue:  A1168  - end of helix
      removed outlier: 3.742A  pdb=" N   ASN A1173 " --> pdb=" O   SER A1169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1205 through 1248
      removed outlier: 3.548A  pdb=" N   VAL A1209 " --> pdb=" O   THR A1205 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   GLN A1218 " --> pdb=" O   SER A1214 " (cutoff:3.500A)
      removed outlier: 4.512A  pdb=" N   THR A1220 " --> pdb=" O   ALA A1216 " (cutoff:3.500A)
      removed outlier: 5.161A  pdb=" N   GLN A1221 " --> pdb=" O   LEU A1217 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   THR A1222 " --> pdb=" O   GLN A1218 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ASN A1224 " --> pdb=" O   THR A1220 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   VAL A1238 " --> pdb=" O   GLU A1234 " (cutoff:3.500A)
      removed outlier: 4.780A  pdb=" N   SER A1239 " --> pdb=" O   THR A1235 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   VAL A1240 " --> pdb=" O   ASN A1236 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   TYR A1246 " --> pdb=" O   ARG A1242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1311 through 1320
      removed outlier: 4.375A  pdb=" N   THR A1316 " --> pdb=" O   LYS A1312 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   LEU A1317 " --> pdb=" O   SER A1313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1338 through 1340
      No H-bonds generated for 'chain 'A' and resid 1338 through 1340'
    Processing helix  chain 'A' and resid 1341 through 1347
    Processing helix  chain 'A' and resid 1363 through 1368
    Processing helix  chain 'A' and resid 1374 through 1385
    Processing helix  chain 'A' and resid 1387 through 1395
    Processing helix  chain 'A' and resid 1397 through 1400
    Processing helix  chain 'A' and resid 1411 through 1426
      removed outlier: 3.679A  pdb=" N   VAL A1426 " --> pdb=" O   ARG A1422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1441 through 1456
    Processing helix  chain 'A' and resid 1467 through 1471
    Processing helix  chain 'A' and resid 1490 through 1498
      removed outlier: 4.044A  pdb=" N   ASN A1498 " --> pdb=" O   LEU A1494 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1500 through 1506
    Processing sheet with id=AA1, first strand: chain 'A' and resid 612 through 615
      removed outlier: 3.609A  pdb=" N   VAL A 689 " --> pdb=" O   GLN A 613 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   THR A 688 " --> pdb=" O   ILE A 628 " (cutoff:3.500A)
      removed outlier: 7.134A  pdb=" N   ILE A 626 " --> pdb=" O   HIS A 690 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   ALA A 653 " --> pdb=" O   ILE A 626 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   ILE A 628 " --> pdb=" O   PHE A 651 " (cutoff:3.500A)
      removed outlier: 6.009A  pdb=" N   PHE A 651 " --> pdb=" O   ILE A 628 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ASP A 630 " --> pdb=" O   ILE A 649 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   ILE A 649 " --> pdb=" O   ASP A 630 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   ALA A 632 " --> pdb=" O   LYS A 647 " (cutoff:3.500A)
      removed outlier: 4.628A  pdb=" N   LYS A 647 " --> pdb=" O   ALA A 632 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 612 through 615
      removed outlier: 3.609A  pdb=" N   VAL A 689 " --> pdb=" O   GLN A 613 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   THR A 688 " --> pdb=" O   ILE A 628 " (cutoff:3.500A)
      removed outlier: 7.134A  pdb=" N   ILE A 626 " --> pdb=" O   HIS A 690 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   THR A 633 " --> pdb=" O   VAL A 683 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   PHE A 681 " --> pdb=" O   LEU A 635 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 693 through 696
      removed outlier: 6.392A  pdb=" N   ASP A 827 " --> pdb=" O   ILE A 831 " (cutoff:3.500A)
      removed outlier: 5.095A  pdb=" N   ILE A 831 " --> pdb=" O   ASP A 827 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 705 through 706
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1289 through 1292
      removed outlier: 5.479A  pdb=" N   LYS A1290 " --> pdb=" O   THR A1279 " (cutoff:3.500A)
      removed outlier: 7.258A  pdb=" N   THR A1279 " --> pdb=" O   LYS A1290 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1289 through 1292
      removed outlier: 5.479A  pdb=" N   LYS A1290 " --> pdb=" O   THR A1279 " (cutoff:3.500A)
      removed outlier: 7.258A  pdb=" N   THR A1279 " --> pdb=" O   LYS A1290 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   ILE A1272 " --> pdb=" O   ILE A1332 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   ILE A1332 " --> pdb=" O   ILE A1272 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   PHE A1274 " --> pdb=" O   ILE A1330 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   ILE A1330 " --> pdb=" O   PHE A1274 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   ASN A1276 " --> pdb=" O   GLY A1328 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   GLY A1328 " --> pdb=" O   ASN A1276 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   SER A1278 " --> pdb=" O   SER A1326 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1350 through 1352
      removed outlier: 6.476A  pdb=" N   LEU A1431 " --> pdb=" O   LEU A1462 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   VAL A1302 " --> pdb=" O   THR A1463 " (cutoff:3.500A)
      removed outlier: 6.117A  pdb=" N   LYS A1301 " --> pdb=" O   ARG A1476 " (cutoff:3.500A)
      removed outlier: 7.670A  pdb=" N   ILE A1478 " --> pdb=" O   LYS A1301 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   GLY A1303 " --> pdb=" O   ILE A1478 " (cutoff:3.500A)
      removed outlier: 7.567A  pdb=" N   LEU A1480 " --> pdb=" O   GLY A1303 " (cutoff:3.500A)
      removed outlier: 7.211A  pdb=" N   VAL A1305 " --> pdb=" O   LEU A1480 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1361 through 1362

    760 hydrogen bonds defined for protein.
    2238 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: 4.48

  Time building geometry restraints manager: 3.28 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1776
        1.31 -     1.43: 3026
        1.43 -     1.56: 6552
        1.56 -     1.68: 5
        1.68 -     1.81: 83
  Bond restraints: 11442
  Sorted by residual:
  bond pdb=" C8  PTY A1602 "
       pdb=" O7  PTY A1602 "
    ideal  model  delta    sigma   weight residual
    1.331  1.398 -0.067 2.00e-02 2.50e+03 1.12e+01
  bond pdb=" C8  PTY A1601 "
       pdb=" O7  PTY A1601 "
    ideal  model  delta    sigma   weight residual
    1.331  1.396 -0.065 2.00e-02 2.50e+03 1.05e+01
  bond pdb=" C30 PTY A1601 "
       pdb=" O4  PTY A1601 "
    ideal  model  delta    sigma   weight residual
    1.331  1.395 -0.064 2.00e-02 2.50e+03 1.04e+01
  bond pdb=" C30 PTY A1602 "
       pdb=" O4  PTY A1602 "
    ideal  model  delta    sigma   weight residual
    1.331  1.392 -0.061 2.00e-02 2.50e+03 9.43e+00
  bond pdb=" CA  VAL A1485 "
       pdb=" CB  VAL A1485 "
    ideal  model  delta    sigma   weight residual
    1.538  1.564 -0.025 1.06e-02 8.90e+03 5.79e+00
  ... (remaining 11437 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.47: 15415
        3.47 -     6.94: 66
        6.94 -    10.41: 9
       10.41 -    13.88: 3
       13.88 -    17.35: 2
  Bond angle restraints: 15495
  Sorted by residual:
  angle pdb=" N   LEU A 646 "
        pdb=" CA  LEU A 646 "
        pdb=" C   LEU A 646 "
      ideal   model   delta    sigma   weight residual
     109.59   97.52   12.07 1.47e+00 4.63e-01 6.74e+01
  angle pdb=" N   LYS A 647 "
        pdb=" CA  LYS A 647 "
        pdb=" C   LYS A 647 "
      ideal   model   delta    sigma   weight residual
     109.14  120.49  -11.35 1.49e+00 4.50e-01 5.80e+01
  angle pdb=" N   LYS A1484 "
        pdb=" CA  LYS A1484 "
        pdb=" C   LYS A1484 "
      ideal   model   delta    sigma   weight residual
     108.96   99.39    9.57 1.59e+00 3.96e-01 3.62e+01
  angle pdb=" O11 PTY A1601 "
        pdb=" P1  PTY A1601 "
        pdb=" O14 PTY A1601 "
      ideal   model   delta    sigma   weight residual
      92.90  110.25  -17.35 3.00e+00 1.11e-01 3.34e+01
  angle pdb=" O11 PTY A1602 "
        pdb=" P1  PTY A1602 "
        pdb=" O14 PTY A1602 "
      ideal   model   delta    sigma   weight residual
      92.90  109.70  -16.80 3.00e+00 1.11e-01 3.14e+01
  ... (remaining 15490 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.90: 6723
       33.90 -    67.80: 115
       67.80 -   101.71: 16
      101.71 -   135.61: 0
      135.61 -   169.51: 1
  Dihedral angle restraints: 6855
    sinusoidal: 2730
      harmonic: 4125
  Sorted by residual:
  dihedral pdb=" CA  LYS A  58 "
           pdb=" C   LYS A  58 "
           pdb=" N   LYS A  59 "
           pdb=" CA  LYS A  59 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.45  -28.55     0      5.00e+00 4.00e-02 3.26e+01
  dihedral pdb=" CA  LEU A1387 "
           pdb=" C   LEU A1387 "
           pdb=" N   LYS A1388 "
           pdb=" CA  LYS A1388 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.95   24.05     0      5.00e+00 4.00e-02 2.31e+01
  dihedral pdb=" CA  ASP A1489 "
           pdb=" C   ASP A1489 "
           pdb=" N   SER A1490 "
           pdb=" CA  SER A1490 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.42  -23.58     0      5.00e+00 4.00e-02 2.22e+01
  ... (remaining 6852 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1370
       0.044 -    0.089: 353
       0.089 -    0.133: 77
       0.133 -    0.177: 3
       0.177 -    0.221: 2
  Chirality restraints: 1805
  Sorted by residual:
  chirality pdb=" CA  LYS A1484 "
            pdb=" N   LYS A1484 "
            pdb=" C   LYS A1484 "
            pdb=" CB  LYS A1484 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.22e+00
  chirality pdb=" CA  LEU A 646 "
            pdb=" N   LEU A 646 "
            pdb=" C   LEU A 646 "
            pdb=" CB  LEU A 646 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" CA  VAL A1485 "
            pdb=" N   VAL A1485 "
            pdb=" C   VAL A1485 "
            pdb=" CB  VAL A1485 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.27    0.17 2.00e-01 2.50e+01 7.19e-01
  ... (remaining 1802 not shown)

  Planarity restraints: 1924
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A1282 "   -0.059 5.00e-02 4.00e+02   8.80e-02 1.24e+01
        pdb=" N   PRO A1283 "    0.152 5.00e-02 4.00e+02
        pdb=" CA  PRO A1283 "   -0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO A1283 "   -0.049 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A  46 "   -0.011 2.00e-02 2.50e+03   2.13e-02 4.55e+00
        pdb=" C   ILE A  46 "    0.037 2.00e-02 2.50e+03
        pdb=" O   ILE A  46 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   THR A  47 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 514 "   -0.010 2.00e-02 2.50e+03   1.99e-02 3.96e+00
        pdb=" C   ARG A 514 "    0.034 2.00e-02 2.50e+03
        pdb=" O   ARG A 514 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   ASN A 515 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1921 not shown)

  Histogram of nonbonded interaction distances:
        1.78 -     2.40: 19
        2.40 -     3.03: 7411
        3.03 -     3.65: 17639
        3.65 -     4.28: 26741
        4.28 -     4.90: 44804
  Nonbonded interactions: 96614
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 836 "
            pdb=" OE1 GLU A 839 "
     model   vdw
     1.781 3.040
  nonbonded pdb=" OG  SER A1022 "
            pdb=" OD1 ASP A1061 "
     model   vdw
     1.904 3.040
  nonbonded pdb=" OD1 ASN A  69 "
            pdb=" N   TRP A  70 "
     model   vdw
     2.136 3.120
  nonbonded pdb=" O   PRO A1298 "
            pdb=" OG1 THR A1460 "
     model   vdw
     2.163 3.040
  nonbonded pdb=" OG  SER A1114 "
            pdb=" NH1 ARG A1118 "
     model   vdw
     2.195 3.120
  ... (remaining 96609 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.500
  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:          0.420
  Check model and map are aligned:         0.080
  Set scattering table:                    0.120
  Process input model:                     29.350
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
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      :  0.005   0.067  11442  Z= 0.219
  Angle     :  0.752  17.350  15495  Z= 0.410
  Chirality :  0.041   0.221   1805
  Planarity :  0.004   0.088   1924
  Dihedral  : 14.012 169.509   4185
  Min Nonbonded Distance : 1.781

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  0.25 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.21), residues: 1386
  helix:  0.54 (0.16), residues: 932
  sheet:  0.25 (0.63), residues: 56
  loop : -0.54 (0.31), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A  70 
 HIS   0.006   0.001   HIS A 364 
 PHE   0.018   0.002   PHE A 954 
 TYR   0.016   0.002   TYR A1105 
 ARG   0.010   0.001   ARG A1035 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10147 (  754)
  hydrogen bonds       : angle       5.74587 ( 2238)
  covalent geometry    : bond        0.00457 (11442)
  covalent geometry    : angle       0.75163 (15495)

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

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

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 213
  time to evaluate  : 1.142 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 ILE cc_start: 0.8538 (mm) cc_final: 0.8253 (mt)
REVERT: A  195 MET cc_start: 0.5187 (ttm) cc_final: 0.4878 (tpp)
REVERT: A  268 LYS cc_start: 0.8290 (pptt) cc_final: 0.8045 (pttt)
REVERT: A  529 MET cc_start: 0.7468 (ttt) cc_final: 0.7158 (ttt)
REVERT: A  777 ASP cc_start: 0.7532 (t0) cc_final: 0.7245 (t70)
REVERT: A 1390 HIS cc_start: 0.5926 (t70) cc_final: 0.5667 (t70)
  outliers start: 2
  outliers final: 2
  residues processed: 215
  average time/residue: 0.2145
  time to fit residues: 68.0851
Evaluate side-chains
  153 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 151
  time to evaluate  : 1.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue 1485 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 118 optimal weight:    3.9990
   chunk 106 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 71 optimal weight:   10.0000
   chunk 56 optimal weight:    3.9990
   chunk 109 optimal weight:    0.6980
   chunk 42 optimal weight:    0.4980
   chunk 66 optimal weight:    0.9980
   chunk 81 optimal weight:    0.3980
   chunk 127 optimal weight:    4.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 132 ASN
** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 613 GLN
A 637 GLN
A 698 GLN
** A1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1107 GLN
A1414 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.176746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.123745 restraints weight = 12327.639|
|-----------------------------------------------------------------------------|
r_work (start): 0.3419 rms_B_bonded: 2.14
r_work: 0.3233 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3082 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7472
moved from start:          0.1455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  11442  Z= 0.178
  Angle     :  0.659   9.155  15495  Z= 0.344
  Chirality :  0.044   0.171   1805
  Planarity :  0.005   0.056   1924
  Dihedral  :  9.093 161.936   1581
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  :  6.17 %
    Favored  : 92.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.22), residues: 1386
  helix:  1.01 (0.16), residues: 936
  sheet:  0.78 (0.68), residues: 56
  loop : -0.24 (0.32), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 163 
 HIS   0.003   0.001   HIS A1026 
 PHE   0.019   0.002   PHE A 464 
 TYR   0.021   0.002   TYR A 695 
 ARG   0.005   0.001   ARG A 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04751 (  754)
  hydrogen bonds       : angle       4.93380 ( 2238)
  covalent geometry    : bond        0.00403 (11442)
  covalent geometry    : angle       0.65882 (15495)

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

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

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 168
  time to evaluate  : 1.151 
Fit side-chains
   revert: symmetry clash
REVERT: A   39 ASN cc_start: 0.7596 (t0) cc_final: 0.7332 (t0)
REVERT: A   43 ILE cc_start: 0.8059 (mm) cc_final: 0.7791 (mt)
REVERT: A   92 ASN cc_start: 0.8018 (t0) cc_final: 0.7748 (t0)
REVERT: A  154 LEU cc_start: 0.8195 (tp) cc_final: 0.7925 (mt)
REVERT: A  167 GLN cc_start: 0.6919 (tt0) cc_final: 0.6455 (mt0)
REVERT: A  242 ASP cc_start: 0.7522 (m-30) cc_final: 0.7195 (m-30)
REVERT: A  268 LYS cc_start: 0.8494 (pptt) cc_final: 0.8075 (pttt)
REVERT: A  462 ASN cc_start: 0.8025 (t0) cc_final: 0.7813 (t0)
REVERT: A  777 ASP cc_start: 0.7994 (t0) cc_final: 0.7710 (t0)
REVERT: A 1280 ARG cc_start: 0.7324 (mtt90) cc_final: 0.7013 (mtt90)
REVERT: A 1394 MET cc_start: 0.6013 (mtt) cc_final: 0.5245 (mmm)
REVERT: A 1424 MET cc_start: 0.8531 (mtm) cc_final: 0.8292 (mtm)
REVERT: A 1472 MET cc_start: 0.7855 (mmm) cc_final: 0.7553 (mmm)
  outliers start: 11
  outliers final: 8
  residues processed: 173
  average time/residue: 0.2067
  time to fit residues: 54.1082
Evaluate side-chains
  154 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 146
  time to evaluate  : 1.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  410 SER
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain A residue  704 ASN
Chi-restraints excluded: chain A residue  712 LEU
Chi-restraints excluded: chain A residue 1123 ILE
Chi-restraints excluded: chain A residue 1146 SER
Chi-restraints excluded: chain A residue 1485 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 93 optimal weight:    0.2980
   chunk 63 optimal weight:    7.9990
   chunk 117 optimal weight:    5.9990
   chunk 90 optimal weight:    0.9980
   chunk 33 optimal weight:    0.3980
   chunk 136 optimal weight:    9.9990
   chunk 101 optimal weight:    1.9990
   chunk 107 optimal weight:    0.5980
   chunk 51 optimal weight:    0.6980
   chunk 138 optimal weight:    0.0980
   chunk 135 optimal weight:    3.9990
   overall best weight:    0.4180

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

Flipped N/Q/H residues before XYZ refinement:
** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 492 ASN
A1147 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.178161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.121057 restraints weight = 12495.926|
|-----------------------------------------------------------------------------|
r_work (start): 0.3426 rms_B_bonded: 2.16
r_work: 0.3297 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3147 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7378
moved from start:          0.1857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11442  Z= 0.139
  Angle     :  0.588   9.048  15495  Z= 0.305
  Chirality :  0.041   0.185   1805
  Planarity :  0.004   0.049   1924
  Dihedral  :  8.293 141.883   1579
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  :  7.57 %
    Favored  : 91.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.22), residues: 1386
  helix:  1.24 (0.16), residues: 940
  sheet:  0.87 (0.70), residues: 55
  loop : -0.24 (0.33), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 163 
 HIS   0.002   0.001   HIS A1020 
 PHE   0.019   0.001   PHE A 464 
 TYR   0.018   0.001   TYR A 722 
 ARG   0.004   0.000   ARG A 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04355 (  754)
  hydrogen bonds       : angle       4.71608 ( 2238)
  covalent geometry    : bond        0.00303 (11442)
  covalent geometry    : angle       0.58836 (15495)

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

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

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 166
  time to evaluate  : 1.264 
Fit side-chains
   revert: symmetry clash
REVERT: A  154 LEU cc_start: 0.8144 (tp) cc_final: 0.7893 (mt)
REVERT: A  167 GLN cc_start: 0.6803 (tt0) cc_final: 0.6413 (mt0)
REVERT: A  195 MET cc_start: 0.5436 (ptm) cc_final: 0.5234 (ptt)
REVERT: A  242 ASP cc_start: 0.7405 (m-30) cc_final: 0.6901 (m-30)
REVERT: A  268 LYS cc_start: 0.8482 (pptt) cc_final: 0.7999 (pttt)
REVERT: A  309 ARG cc_start: 0.7729 (ttt180) cc_final: 0.6880 (ttp80)
REVERT: A  462 ASN cc_start: 0.8015 (t0) cc_final: 0.7789 (t0)
REVERT: A  516 ASN cc_start: 0.7998 (t0) cc_final: 0.7642 (m-40)
REVERT: A  777 ASP cc_start: 0.8134 (t0) cc_final: 0.7726 (t0)
REVERT: A 1241 GLU cc_start: 0.8104 (tt0) cc_final: 0.7490 (tp30)
REVERT: A 1280 ARG cc_start: 0.7154 (mtt90) cc_final: 0.6860 (mtt90)
REVERT: A 1360 GLU cc_start: 0.6935 (mt-10) cc_final: 0.6589 (mt-10)
REVERT: A 1394 MET cc_start: 0.5762 (mtt) cc_final: 0.5095 (mmm)
REVERT: A 1424 MET cc_start: 0.8551 (mtm) cc_final: 0.8313 (mtm)
REVERT: A 1472 MET cc_start: 0.7788 (mmm) cc_final: 0.7447 (mmm)
  outliers start: 17
  outliers final: 11
  residues processed: 176
  average time/residue: 0.2184
  time to fit residues: 57.0083
Evaluate side-chains
  162 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 151
  time to evaluate  : 1.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  586 ASN
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain A residue  704 ASN
Chi-restraints excluded: chain A residue  712 LEU
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  980 SER
Chi-restraints excluded: chain A residue 1100 SER
Chi-restraints excluded: chain A residue 1146 SER
Chi-restraints excluded: chain A residue 1147 GLN
Chi-restraints excluded: chain A residue 1229 MET
Chi-restraints excluded: chain A residue 1485 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 84 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 75 optimal weight:    0.4980
   chunk 126 optimal weight:    7.9990
   chunk 123 optimal weight:    0.7980
   chunk 48 optimal weight:    4.9990
   chunk 47 optimal weight:    0.8980
   chunk 23 optimal weight:    0.6980
   chunk 21 optimal weight:    0.8980
   chunk 11 optimal weight:    4.9990
   chunk 121 optimal weight:    4.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 359 GLN
A 657 ASN
A1449 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.176718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.124742 restraints weight = 12377.381|
|-----------------------------------------------------------------------------|
r_work (start): 0.3462 rms_B_bonded: 2.18
r_work: 0.3243 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3091 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7509
moved from start:          0.2100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  11442  Z= 0.170
  Angle     :  0.589   8.911  15495  Z= 0.306
  Chirality :  0.042   0.188   1805
  Planarity :  0.004   0.052   1924
  Dihedral  :  7.861 125.209   1579
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  :  9.30 %
    Favored  : 88.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.18 (0.22), residues: 1386
  helix:  1.27 (0.16), residues: 939
  sheet:  0.85 (0.69), residues: 55
  loop : -0.28 (0.33), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A  70 
 HIS   0.003   0.001   HIS A 364 
 PHE   0.023   0.002   PHE A 713 
 TYR   0.016   0.001   TYR A1105 
 ARG   0.004   0.000   ARG A 156 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04367 (  754)
  hydrogen bonds       : angle       4.69997 ( 2238)
  covalent geometry    : bond        0.00394 (11442)
  covalent geometry    : angle       0.58931 (15495)

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

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

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 153
  time to evaluate  : 1.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  154 LEU cc_start: 0.8215 (tp) cc_final: 0.7935 (mt)
REVERT: A  167 GLN cc_start: 0.6910 (tt0) cc_final: 0.6525 (mt0)
REVERT: A  268 LYS cc_start: 0.8508 (pptt) cc_final: 0.7966 (pttt)
REVERT: A  309 ARG cc_start: 0.7849 (ttt180) cc_final: 0.6963 (ttp80)
REVERT: A  462 ASN cc_start: 0.8148 (t0) cc_final: 0.7909 (t0)
REVERT: A  516 ASN cc_start: 0.8049 (t0) cc_final: 0.7734 (m-40)
REVERT: A  721 PHE cc_start: 0.8458 (t80) cc_final: 0.8064 (t80)
REVERT: A  777 ASP cc_start: 0.8292 (t0) cc_final: 0.7890 (t0)
REVERT: A  962 MET cc_start: 0.8050 (tpp) cc_final: 0.7714 (tpp)
REVERT: A 1181 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8119 (mt-10)
REVERT: A 1360 GLU cc_start: 0.6918 (mt-10) cc_final: 0.6712 (mt-10)
REVERT: A 1394 MET cc_start: 0.5932 (mtt) cc_final: 0.5313 (mmm)
REVERT: A 1424 MET cc_start: 0.8659 (mtm) cc_final: 0.8263 (mtm)
REVERT: A 1472 MET cc_start: 0.7844 (mmm) cc_final: 0.7460 (mmm)
  outliers start: 22
  outliers final: 15
  residues processed: 164
  average time/residue: 0.1952
  time to fit residues: 49.2371
Evaluate side-chains
  158 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 143
  time to evaluate  : 1.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  410 SER
Chi-restraints excluded: chain A residue  448 MET
Chi-restraints excluded: chain A residue  586 ASN
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  595 ILE
Chi-restraints excluded: chain A residue  624 VAL
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain A residue  712 LEU
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  980 SER
Chi-restraints excluded: chain A residue 1100 SER
Chi-restraints excluded: chain A residue 1123 ILE
Chi-restraints excluded: chain A residue 1146 SER
Chi-restraints excluded: chain A residue 1229 MET
Chi-restraints excluded: chain A residue 1485 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 10 optimal weight:    0.6980
   chunk 101 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   chunk 120 optimal weight:    0.9980
   chunk 79 optimal weight:    5.9990
   chunk 128 optimal weight:    7.9990
   chunk 48 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 106 optimal weight:    0.9980
   chunk 115 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 637 GLN
A1055 ASN
A1147 GLN
A1260 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.175093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.123788 restraints weight = 12381.235|
|-----------------------------------------------------------------------------|
r_work (start): 0.3455 rms_B_bonded: 2.16
r_work: 0.3227 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3075 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7534
moved from start:          0.2333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  11442  Z= 0.183
  Angle     :  0.585   8.879  15495  Z= 0.303
  Chirality :  0.042   0.188   1805
  Planarity :  0.004   0.054   1924
  Dihedral  :  7.403 100.014   1579
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 10.78 %
    Favored  : 87.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.22), residues: 1386
  helix:  1.29 (0.16), residues: 938
  sheet:  0.91 (0.70), residues: 55
  loop : -0.31 (0.32), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A  70 
 HIS   0.005   0.001   HIS A 364 
 PHE   0.020   0.002   PHE A 464 
 TYR   0.018   0.001   TYR A1105 
 ARG   0.004   0.000   ARG A1280 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04374 (  754)
  hydrogen bonds       : angle       4.66936 ( 2238)
  covalent geometry    : bond        0.00426 (11442)
  covalent geometry    : angle       0.58459 (15495)

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

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

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 150
  time to evaluate  : 1.202 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  154 LEU cc_start: 0.8237 (tp) cc_final: 0.7957 (mt)
REVERT: A  167 GLN cc_start: 0.6900 (tt0) cc_final: 0.6567 (mt0)
REVERT: A  309 ARG cc_start: 0.7879 (ttt180) cc_final: 0.6974 (ttp80)
REVERT: A  462 ASN cc_start: 0.8192 (t0) cc_final: 0.7969 (t0)
REVERT: A  469 GLN cc_start: 0.5973 (mm110) cc_final: 0.5554 (mp10)
REVERT: A  516 ASN cc_start: 0.8116 (t0) cc_final: 0.7822 (m-40)
REVERT: A  529 MET cc_start: 0.7413 (ttt) cc_final: 0.7122 (ttt)
REVERT: A  721 PHE cc_start: 0.8466 (t80) cc_final: 0.8175 (t80)
REVERT: A  777 ASP cc_start: 0.8338 (t0) cc_final: 0.7954 (t0)
REVERT: A  834 GLN cc_start: 0.6551 (tp40) cc_final: 0.6258 (tp40)
REVERT: A  962 MET cc_start: 0.8136 (tpp) cc_final: 0.7863 (tpp)
REVERT: A 1181 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8152 (mt-10)
REVERT: A 1250 LYS cc_start: 0.8305 (tppt) cc_final: 0.7855 (tptp)
REVERT: A 1360 GLU cc_start: 0.6886 (mt-10) cc_final: 0.6629 (mt-10)
REVERT: A 1390 HIS cc_start: 0.6521 (t70) cc_final: 0.5881 (t-90)
REVERT: A 1394 MET cc_start: 0.5947 (mtt) cc_final: 0.5379 (mmt)
REVERT: A 1424 MET cc_start: 0.8669 (mtm) cc_final: 0.8223 (mtm)
REVERT: A 1472 MET cc_start: 0.7895 (mmm) cc_final: 0.7484 (mmm)
  outliers start: 26
  outliers final: 16
  residues processed: 163
  average time/residue: 0.1979
  time to fit residues: 48.8321
Evaluate side-chains
  155 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 139
  time to evaluate  : 1.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 GLU
Chi-restraints excluded: chain A residue  410 SER
Chi-restraints excluded: chain A residue  448 MET
Chi-restraints excluded: chain A residue  586 ASN
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  595 ILE
Chi-restraints excluded: chain A residue  624 VAL
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain A residue  712 LEU
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  980 SER
Chi-restraints excluded: chain A residue 1100 SER
Chi-restraints excluded: chain A residue 1123 ILE
Chi-restraints excluded: chain A residue 1146 SER
Chi-restraints excluded: chain A residue 1147 GLN
Chi-restraints excluded: chain A residue 1485 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 87 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 92 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9990
   chunk 88 optimal weight:    0.5980
   chunk 24 optimal weight:    2.9990
   chunk 123 optimal weight:    0.7980
   chunk 118 optimal weight:    0.6980
   chunk 25 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
A 637 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.175652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.124186 restraints weight = 12523.211|
|-----------------------------------------------------------------------------|
r_work (start): 0.3456 rms_B_bonded: 2.19
r_work: 0.3226 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3074 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.2429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  11442  Z= 0.176
  Angle     :  0.587   8.928  15495  Z= 0.302
  Chirality :  0.042   0.192   1805
  Planarity :  0.004   0.055   1924
  Dihedral  :  7.100  86.109   1579
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 12.10 %
    Favored  : 86.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.22), residues: 1386
  helix:  1.32 (0.16), residues: 937
  sheet:  0.93 (0.69), residues: 55
  loop : -0.28 (0.32), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 636 
 HIS   0.005   0.001   HIS A 364 
 PHE   0.021   0.001   PHE A 464 
 TYR   0.016   0.001   TYR A1105 
 ARG   0.005   0.000   ARG A1280 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04309 (  754)
  hydrogen bonds       : angle       4.67605 ( 2238)
  covalent geometry    : bond        0.00409 (11442)
  covalent geometry    : angle       0.58748 (15495)

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

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

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 147
  time to evaluate  : 1.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  154 LEU cc_start: 0.8231 (tp) cc_final: 0.7961 (mt)
REVERT: A  167 GLN cc_start: 0.6858 (tt0) cc_final: 0.6558 (mt0)
REVERT: A  309 ARG cc_start: 0.7878 (ttt180) cc_final: 0.6979 (ttp80)
REVERT: A  462 ASN cc_start: 0.8197 (t0) cc_final: 0.7974 (t0)
REVERT: A  469 GLN cc_start: 0.5982 (mm110) cc_final: 0.5578 (mp10)
REVERT: A  516 ASN cc_start: 0.8230 (t0) cc_final: 0.7898 (m-40)
REVERT: A  529 MET cc_start: 0.7444 (ttt) cc_final: 0.7205 (ttt)
REVERT: A  605 GLU cc_start: 0.8525 (pt0) cc_final: 0.8316 (pt0)
REVERT: A  631 ASP cc_start: 0.5750 (t0) cc_final: 0.5414 (t0)
REVERT: A  721 PHE cc_start: 0.8459 (t80) cc_final: 0.8257 (t80)
REVERT: A  777 ASP cc_start: 0.8373 (t0) cc_final: 0.8019 (t0)
REVERT: A  962 MET cc_start: 0.8154 (tpp) cc_final: 0.7915 (tpp)
REVERT: A 1250 LYS cc_start: 0.8296 (tppt) cc_final: 0.7851 (tptp)
REVERT: A 1280 ARG cc_start: 0.7212 (mtt90) cc_final: 0.7004 (mtt90)
REVERT: A 1360 GLU cc_start: 0.6943 (mt-10) cc_final: 0.6666 (mt-10)
REVERT: A 1394 MET cc_start: 0.5954 (mtt) cc_final: 0.5368 (mmp)
REVERT: A 1424 MET cc_start: 0.8603 (mtm) cc_final: 0.8281 (mtm)
REVERT: A 1472 MET cc_start: 0.7888 (mmm) cc_final: 0.7459 (mmm)
  outliers start: 22
  outliers final: 15
  residues processed: 162
  average time/residue: 0.2020
  time to fit residues: 49.4562
Evaluate side-chains
  152 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 137
  time to evaluate  : 1.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 GLU
Chi-restraints excluded: chain A residue  410 SER
Chi-restraints excluded: chain A residue  586 ASN
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  595 ILE
Chi-restraints excluded: chain A residue  624 VAL
Chi-restraints excluded: chain A residue  637 GLN
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain A residue  712 LEU
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  980 SER
Chi-restraints excluded: chain A residue 1100 SER
Chi-restraints excluded: chain A residue 1123 ILE
Chi-restraints excluded: chain A residue 1146 SER
Chi-restraints excluded: chain A residue 1485 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 63 optimal weight:    3.9990
   chunk 32 optimal weight:    0.5980
   chunk 19 optimal weight:    0.0270
   chunk 27 optimal weight:    0.6980
   chunk 81 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9980
   chunk 105 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9980
   chunk 20 optimal weight:    0.1980
   chunk 77 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.4438

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

Flipped N/Q/H residues before XYZ refinement:
A 210 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.177309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.125231 restraints weight = 12521.691|
|-----------------------------------------------------------------------------|
r_work (start): 0.3467 rms_B_bonded: 2.24
r_work: 0.3248 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3093 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7504
moved from start:          0.2581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11442  Z= 0.135
  Angle     :  0.564   8.831  15495  Z= 0.289
  Chirality :  0.041   0.196   1805
  Planarity :  0.004   0.054   1924
  Dihedral  :  6.762  84.962   1579
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 13.17 %
    Favored  : 85.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.22), residues: 1386
  helix:  1.47 (0.16), residues: 937
  sheet:  0.94 (0.70), residues: 55
  loop : -0.31 (0.32), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 636 
 HIS   0.004   0.001   HIS A1390 
 PHE   0.023   0.001   PHE A 464 
 TYR   0.015   0.001   TYR A1105 
 ARG   0.007   0.000   ARG A 638 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04126 (  754)
  hydrogen bonds       : angle       4.58743 ( 2238)
  covalent geometry    : bond        0.00297 (11442)
  covalent geometry    : angle       0.56422 (15495)

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

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

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 149
  time to evaluate  : 1.131 
Fit side-chains
   revert: symmetry clash
REVERT: A  154 LEU cc_start: 0.8119 (tp) cc_final: 0.7886 (mt)
REVERT: A  164 TYR cc_start: 0.6300 (m-10) cc_final: 0.5998 (m-10)
REVERT: A  167 GLN cc_start: 0.6650 (tt0) cc_final: 0.6406 (mt0)
REVERT: A  309 ARG cc_start: 0.7887 (ttt180) cc_final: 0.6996 (ttp80)
REVERT: A  462 ASN cc_start: 0.8183 (t0) cc_final: 0.7960 (t0)
REVERT: A  469 GLN cc_start: 0.5921 (mm110) cc_final: 0.5612 (mp10)
REVERT: A  516 ASN cc_start: 0.8233 (t0) cc_final: 0.7906 (m-40)
REVERT: A  631 ASP cc_start: 0.5726 (t0) cc_final: 0.5347 (t0)
REVERT: A  637 GLN cc_start: 0.7085 (tt0) cc_final: 0.6193 (tt0)
REVERT: A  777 ASP cc_start: 0.8386 (t0) cc_final: 0.8014 (t0)
REVERT: A  962 MET cc_start: 0.8177 (tpp) cc_final: 0.7965 (tpp)
REVERT: A 1176 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.7993 (tp)
REVERT: A 1181 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8285 (mt-10)
REVERT: A 1250 LYS cc_start: 0.8223 (tppt) cc_final: 0.7771 (tptp)
REVERT: A 1360 GLU cc_start: 0.6931 (mt-10) cc_final: 0.6689 (mt-10)
REVERT: A 1390 HIS cc_start: 0.6164 (t70) cc_final: 0.5839 (t-90)
REVERT: A 1394 MET cc_start: 0.6083 (mtt) cc_final: 0.5524 (mmm)
REVERT: A 1424 MET cc_start: 0.8608 (mtm) cc_final: 0.8216 (mtm)
REVERT: A 1472 MET cc_start: 0.7899 (mmm) cc_final: 0.7487 (mmm)
  outliers start: 21
  outliers final: 14
  residues processed: 163
  average time/residue: 0.1961
  time to fit residues: 48.5441
Evaluate side-chains
  150 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 135
  time to evaluate  : 1.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 GLU
Chi-restraints excluded: chain A residue  586 ASN
Chi-restraints excluded: chain A residue  595 ILE
Chi-restraints excluded: chain A residue  624 VAL
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain A residue  712 LEU
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  967 MET
Chi-restraints excluded: chain A residue  980 SER
Chi-restraints excluded: chain A residue 1100 SER
Chi-restraints excluded: chain A residue 1123 ILE
Chi-restraints excluded: chain A residue 1146 SER
Chi-restraints excluded: chain A residue 1147 GLN
Chi-restraints excluded: chain A residue 1176 LEU
Chi-restraints excluded: chain A residue 1485 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   chunk 54 optimal weight:    0.6980
   chunk 107 optimal weight:    0.1980
   chunk 4 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 102 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 47 optimal weight:    0.4980
   chunk 82 optimal weight:   10.0000
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 424 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.176784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.118516 restraints weight = 12589.384|
|-----------------------------------------------------------------------------|
r_work (start): 0.3396 rms_B_bonded: 2.28
r_work: 0.3269 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3116 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7447
moved from start:          0.2743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11442  Z= 0.144
  Angle     :  0.570   9.516  15495  Z= 0.292
  Chirality :  0.041   0.202   1805
  Planarity :  0.004   0.054   1924
  Dihedral  :  6.494  82.950   1579
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 13.99 %
    Favored  : 84.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.22), residues: 1386
  helix:  1.51 (0.16), residues: 939
  sheet:  0.97 (0.71), residues: 55
  loop : -0.29 (0.32), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 636 
 HIS   0.004   0.001   HIS A1390 
 PHE   0.027   0.001   PHE A 464 
 TYR   0.016   0.001   TYR A1105 
 ARG   0.005   0.000   ARG A1280 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04124 (  754)
  hydrogen bonds       : angle       4.53968 ( 2238)
  covalent geometry    : bond        0.00324 (11442)
  covalent geometry    : angle       0.56961 (15495)

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

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

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 148
  time to evaluate  : 1.143 
Fit side-chains
   revert: symmetry clash
REVERT: A  154 LEU cc_start: 0.8083 (tp) cc_final: 0.7883 (mt)
REVERT: A  164 TYR cc_start: 0.6400 (m-10) cc_final: 0.6075 (m-10)
REVERT: A  309 ARG cc_start: 0.7828 (ttt180) cc_final: 0.6912 (ttp80)
REVERT: A  462 ASN cc_start: 0.8160 (t0) cc_final: 0.7932 (t0)
REVERT: A  466 MET cc_start: 0.7898 (tmm) cc_final: 0.7679 (tmm)
REVERT: A  469 GLN cc_start: 0.5874 (mm110) cc_final: 0.5634 (mp10)
REVERT: A  516 ASN cc_start: 0.8211 (t0) cc_final: 0.7873 (m-40)
REVERT: A  631 ASP cc_start: 0.5733 (t0) cc_final: 0.5329 (t0)
REVERT: A  777 ASP cc_start: 0.8392 (t0) cc_final: 0.8012 (t0)
REVERT: A  962 MET cc_start: 0.8127 (tpp) cc_final: 0.7914 (tpp)
REVERT: A 1176 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.7920 (tp)
REVERT: A 1181 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8154 (mt-10)
REVERT: A 1250 LYS cc_start: 0.8134 (tppt) cc_final: 0.7753 (tptp)
REVERT: A 1360 GLU cc_start: 0.6912 (mt-10) cc_final: 0.6689 (mt-10)
REVERT: A 1390 HIS cc_start: 0.5996 (t70) cc_final: 0.5485 (t-90)
REVERT: A 1394 MET cc_start: 0.6062 (mtt) cc_final: 0.5609 (mmt)
REVERT: A 1424 MET cc_start: 0.8565 (mtm) cc_final: 0.8206 (mtm)
REVERT: A 1472 MET cc_start: 0.7897 (mmm) cc_final: 0.7501 (mmm)
  outliers start: 17
  outliers final: 16
  residues processed: 159
  average time/residue: 0.2005
  time to fit residues: 48.3634
Evaluate side-chains
  152 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 135
  time to evaluate  : 1.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 GLU
Chi-restraints excluded: chain A residue  410 SER
Chi-restraints excluded: chain A residue  586 ASN
Chi-restraints excluded: chain A residue  595 ILE
Chi-restraints excluded: chain A residue  624 VAL
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain A residue  712 LEU
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  967 MET
Chi-restraints excluded: chain A residue  980 SER
Chi-restraints excluded: chain A residue 1009 GLN
Chi-restraints excluded: chain A residue 1123 ILE
Chi-restraints excluded: chain A residue 1146 SER
Chi-restraints excluded: chain A residue 1147 GLN
Chi-restraints excluded: chain A residue 1176 LEU
Chi-restraints excluded: chain A residue 1403 LEU
Chi-restraints excluded: chain A residue 1485 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 113 optimal weight:    1.9990
   chunk 98 optimal weight:    0.5980
   chunk 47 optimal weight:    0.0770
   chunk 139 optimal weight:   10.0000
   chunk 81 optimal weight:    1.9990
   chunk 95 optimal weight:    0.4980
   chunk 29 optimal weight:    0.4980
   chunk 25 optimal weight:    0.3980
   chunk 126 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9990
   chunk 57 optimal weight:    0.8980
   overall best weight:    0.4138

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.178019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.126379 restraints weight = 12567.662|
|-----------------------------------------------------------------------------|
r_work (start): 0.3479 rms_B_bonded: 2.34
r_work: 0.3247 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3093 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7486
moved from start:          0.2888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  11442  Z= 0.133
  Angle     :  0.569   9.707  15495  Z= 0.290
  Chirality :  0.040   0.198   1805
  Planarity :  0.004   0.054   1924
  Dihedral  :  6.250  80.583   1579
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 14.57 %
    Favored  : 83.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.22), residues: 1386
  helix:  1.58 (0.17), residues: 941
  sheet:  0.89 (0.70), residues: 55
  loop : -0.26 (0.32), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  70 
 HIS   0.004   0.001   HIS A1390 
 PHE   0.027   0.001   PHE A 464 
 TYR   0.015   0.001   TYR A1105 
 ARG   0.006   0.000   ARG A1321 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04024 (  754)
  hydrogen bonds       : angle       4.49112 ( 2238)
  covalent geometry    : bond        0.00292 (11442)
  covalent geometry    : angle       0.56850 (15495)

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

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

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 145
  time to evaluate  : 1.139 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  309 ARG cc_start: 0.7849 (ttt180) cc_final: 0.6975 (ttp80)
REVERT: A  462 ASN cc_start: 0.8171 (t0) cc_final: 0.7912 (t0)
REVERT: A  466 MET cc_start: 0.7913 (tmm) cc_final: 0.7691 (tmm)
REVERT: A  469 GLN cc_start: 0.5873 (mm110) cc_final: 0.5656 (mp10)
REVERT: A  516 ASN cc_start: 0.8272 (t0) cc_final: 0.7904 (m-40)
REVERT: A  631 ASP cc_start: 0.5748 (t0) cc_final: 0.5326 (t0)
REVERT: A  777 ASP cc_start: 0.8392 (t0) cc_final: 0.8000 (t0)
REVERT: A 1176 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8028 (tp)
REVERT: A 1250 LYS cc_start: 0.8099 (tppt) cc_final: 0.7744 (tptp)
REVERT: A 1280 ARG cc_start: 0.7009 (mtt90) cc_final: 0.6776 (mtt90)
REVERT: A 1390 HIS cc_start: 0.6157 (t70) cc_final: 0.5425 (t-90)
REVERT: A 1394 MET cc_start: 0.5927 (mtt) cc_final: 0.5519 (mmt)
REVERT: A 1424 MET cc_start: 0.8622 (mtm) cc_final: 0.8232 (mtm)
REVERT: A 1472 MET cc_start: 0.7887 (mmm) cc_final: 0.7476 (mmm)
  outliers start: 21
  outliers final: 19
  residues processed: 158
  average time/residue: 0.2069
  time to fit residues: 48.8075
Evaluate side-chains
  160 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 140
  time to evaluate  : 1.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 GLU
Chi-restraints excluded: chain A residue  137 PHE
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  410 SER
Chi-restraints excluded: chain A residue  586 ASN
Chi-restraints excluded: chain A residue  595 ILE
Chi-restraints excluded: chain A residue  624 VAL
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain A residue  712 LEU
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  967 MET
Chi-restraints excluded: chain A residue  980 SER
Chi-restraints excluded: chain A residue 1009 GLN
Chi-restraints excluded: chain A residue 1100 SER
Chi-restraints excluded: chain A residue 1123 ILE
Chi-restraints excluded: chain A residue 1147 GLN
Chi-restraints excluded: chain A residue 1176 LEU
Chi-restraints excluded: chain A residue 1305 VAL
Chi-restraints excluded: chain A residue 1386 HIS
Chi-restraints excluded: chain A residue 1485 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 61 optimal weight:    0.0870
   chunk 39 optimal weight:    0.1980
   chunk 53 optimal weight:    0.9980
   chunk 45 optimal weight:    0.5980
   chunk 112 optimal weight:    0.8980
   chunk 60 optimal weight:    0.7980
   chunk 107 optimal weight:    0.9980
   chunk 34 optimal weight:    0.1980
   chunk 15 optimal weight:    3.9990
   chunk 25 optimal weight:    0.1980
   chunk 41 optimal weight:    0.1980
   overall best weight:    0.1758

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

Flipped N/Q/H residues before XYZ refinement:
A 364 HIS
A 469 GLN
A 985 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.180720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.123563 restraints weight = 12445.420|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 2.26
r_work: 0.3304 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3155 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7330
moved from start:          0.3138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.051  11442  Z= 0.117
  Angle     :  0.557   9.750  15495  Z= 0.284
  Chirality :  0.040   0.193   1805
  Planarity :  0.004   0.053   1924
  Dihedral  :  5.981  77.931   1579
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 15.14 %
    Favored  : 83.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.65 (0.23), residues: 1386
  helix:  1.68 (0.17), residues: 947
  sheet:  0.77 (0.68), residues: 55
  loop : -0.25 (0.33), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A  70 
 HIS   0.004   0.001   HIS A1390 
 PHE   0.030   0.001   PHE A 464 
 TYR   0.014   0.001   TYR A1105 
 ARG   0.003   0.000   ARG A1280 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03865 (  754)
  hydrogen bonds       : angle       4.41512 ( 2238)
  covalent geometry    : bond        0.00246 (11442)
  covalent geometry    : angle       0.55671 (15495)

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

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

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 151
  time to evaluate  : 1.140 
Fit side-chains
   revert: symmetry clash
REVERT: A   34 ASP cc_start: 0.7637 (m-30) cc_final: 0.7390 (t0)
REVERT: A   76 MET cc_start: 0.8279 (mmm) cc_final: 0.7930 (mmm)
REVERT: A  309 ARG cc_start: 0.7700 (ttt180) cc_final: 0.6822 (ttp80)
REVERT: A  466 MET cc_start: 0.7846 (tmm) cc_final: 0.7625 (tmm)
REVERT: A  516 ASN cc_start: 0.8162 (t0) cc_final: 0.7831 (m-40)
REVERT: A  606 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7631 (mm-30)
REVERT: A  631 ASP cc_start: 0.5699 (t0) cc_final: 0.5271 (t0)
REVERT: A  777 ASP cc_start: 0.8344 (t0) cc_final: 0.7935 (t0)
REVERT: A 1176 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8089 (tp)
REVERT: A 1181 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8068 (mt-10)
REVERT: A 1250 LYS cc_start: 0.8087 (tppt) cc_final: 0.7772 (tptp)
REVERT: A 1280 ARG cc_start: 0.6896 (mtt90) cc_final: 0.6608 (mtt90)
REVERT: A 1390 HIS cc_start: 0.6419 (t70) cc_final: 0.5737 (t-90)
REVERT: A 1394 MET cc_start: 0.6052 (mtt) cc_final: 0.5708 (mmt)
REVERT: A 1424 MET cc_start: 0.8577 (mtm) cc_final: 0.8202 (mtm)
REVERT: A 1472 MET cc_start: 0.7991 (mmm) cc_final: 0.7645 (mmm)
  outliers start: 14
  outliers final: 11
  residues processed: 159
  average time/residue: 0.2306
  time to fit residues: 53.6334
Evaluate side-chains
  151 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 139
  time to evaluate  : 1.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 GLU
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  595 ILE
Chi-restraints excluded: chain A residue  624 VAL
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue 1009 GLN
Chi-restraints excluded: chain A residue 1100 SER
Chi-restraints excluded: chain A residue 1147 GLN
Chi-restraints excluded: chain A residue 1176 LEU
Chi-restraints excluded: chain A residue 1386 HIS
Chi-restraints excluded: chain A residue 1485 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 113 optimal weight:    0.8980
   chunk 100 optimal weight:    0.5980
   chunk 37 optimal weight:    3.9990
   chunk 137 optimal weight:    7.9990
   chunk 35 optimal weight:    1.9990
   chunk 108 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9990
   chunk 139 optimal weight:   10.0000
   chunk 25 optimal weight:    0.0770
   chunk 83 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
A 535 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.177641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.119724 restraints weight = 12473.453|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 2.26
r_work: 0.3282 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3132 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7427
moved from start:          0.3119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  11442  Z= 0.151
  Angle     :  0.586  12.105  15495  Z= 0.296
  Chirality :  0.041   0.193   1805
  Planarity :  0.004   0.054   1924
  Dihedral  :  5.945  75.003   1579
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 15.14 %
    Favored  : 83.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.60 (0.22), residues: 1386
  helix:  1.65 (0.17), residues: 945
  sheet:  0.71 (0.68), residues: 55
  loop : -0.24 (0.32), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A  70 
 HIS   0.003   0.001   HIS A 364 
 PHE   0.034   0.002   PHE A 464 
 TYR   0.019   0.001   TYR A1105 
 ARG   0.004   0.000   ARG A1280 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04053 (  754)
  hydrogen bonds       : angle       4.46906 ( 2238)
  covalent geometry    : bond        0.00346 (11442)
  covalent geometry    : angle       0.58602 (15495)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6714.94 seconds
wall clock time: 116 minutes 49.76 seconds (7009.76 seconds total)