Starting phenix.real_space_refine
on Thu Jun 12 23:15:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y1o_38841/06_2025/8y1o_38841.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y1o_38841/06_2025/8y1o_38841.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.92
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8y1o_38841/06_2025/8y1o_38841.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y1o_38841/06_2025/8y1o_38841.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y1o_38841/06_2025/8y1o_38841.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y1o_38841/06_2025/8y1o_38841.cif"
  }
  resolution = 3.92
  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=   0.001 sd=   0.024
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      64      5.16       5
     C    9155      2.51       5
     N    2511      2.21       5
     O    2496      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 14226
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 14226
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1844, 14226
          Classifications: {'peptide': 1844}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 113, 'TRANS': 1730}
          Chain breaks: 8
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 18
  Time building chain proxies: 9.73, per 1000 atoms: 0.68
  Number of scatterers: 14226
  At special positions: 0
  Unit cell: (84.53, 100.58, 215.07, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      64     16.00
     O    2496      8.00
     N    2511      7.00
     C    9155      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  54 " - pdb=" SG  CYS A  81 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  75 " - pdb=" SG  CYS A 225 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 267 " - pdb=" SG  CYS A 406 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A1017 " - pdb=" SG  CYS A1150 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1345 " - pdb=" SG  CYS A1359 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.67
  Conformation dependent library (CDL) restraints added in 2.0 seconds
  

  3652 Ramachandran restraints generated.
    1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3378

  Finding SS restraints...
    Secondary structure from input PDB file:
      80 helices and 10 sheets defined
      56.6% alpha, 5.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.06
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 21
      removed outlier: 3.628A  pdb=" N   MET A   8 " --> pdb=" O   TRP A   4 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   TYR A  17 " --> pdb=" O   LYS A  13 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ARG A  18 " --> pdb=" O   ASN A  14 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 21 through 46
      removed outlier: 3.972A  pdb=" N   LEU A  25 " --> pdb=" O   GLN A  21 " (cutoff:3.500A)
      Proline residue:  A  32  - end of helix
    Processing helix  chain 'A' and resid 62 through 65
      removed outlier: 3.849A  pdb=" N   GLY A  65 " --> pdb=" O   PRO A  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 62 through 65'
    Processing helix  chain 'A' and resid 66 through 76
    Processing helix  chain 'A' and resid 86 through 90
    Processing helix  chain 'A' and resid 100 through 113
    Processing helix  chain 'A' and resid 117 through 135
      removed outlier: 4.116A  pdb=" N   ALA A 123 " --> pdb=" O   HIS A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 196
    Processing helix  chain 'A' and resid 197 through 208
      removed outlier: 4.306A  pdb=" N   VAL A 201 " --> pdb=" O   LEU A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 225
      removed outlier: 3.943A  pdb=" N   ALA A 223 " --> pdb=" O   LEU A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 277
      removed outlier: 4.043A  pdb=" N   HIS A 277 " --> pdb=" O   ALA A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 286
    Processing helix  chain 'A' and resid 287 through 292
    Processing helix  chain 'A' and resid 301 through 312
    Processing helix  chain 'A' and resid 313 through 315
      No H-bonds generated for 'chain 'A' and resid 313 through 315'
    Processing helix  chain 'A' and resid 319 through 338
      removed outlier: 3.992A  pdb=" N   ASP A 323 " --> pdb=" O   THR A 319 " (cutoff:3.500A)
      Proline residue:  A 333  - end of helix
    Processing helix  chain 'A' and resid 343 through 352
      removed outlier: 4.060A  pdb=" N   LEU A 348 " --> pdb=" O   ASN A 344 " (cutoff:3.500A)
      removed outlier: 5.037A  pdb=" N   GLN A 349 " --> pdb=" O   VAL A 345 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ARG A 350 " --> pdb=" O   ALA A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 377
    Processing helix  chain 'A' and resid 386 through 404
    Processing helix  chain 'A' and resid 417 through 431
    Processing helix  chain 'A' and resid 503 through 520
      removed outlier: 3.571A  pdb=" N   GLY A 520 " --> pdb=" O   ARG A 516 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 541 through 546
    Processing helix  chain 'A' and resid 549 through 558
      removed outlier: 3.598A  pdb=" N   THR A 555 " --> pdb=" O   PRO A 551 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 564 through 575
    Processing helix  chain 'A' and resid 576 through 585
      removed outlier: 3.559A  pdb=" N   THR A 580 " --> pdb=" O   ARG A 576 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   GLY A 585 " --> pdb=" O   MET A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 617
      removed outlier: 4.227A  pdb=" N   GLY A 601 " --> pdb=" O   LEU A 597 " (cutoff:3.500A)
      Proline residue:  A 602  - end of helix
      removed outlier: 3.832A  pdb=" N   LEU A 614 " --> pdb=" O   LEU A 610 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 624 through 648
      removed outlier: 3.951A  pdb=" N   VAL A 628 " --> pdb=" O   HIS A 624 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   THR A 641 " --> pdb=" O   VAL A 637 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   GLN A 642 " --> pdb=" O   ALA A 638 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 652 through 666
      removed outlier: 4.369A  pdb=" N   GLY A 661 " --> pdb=" O   ALA A 657 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   LEU A 662 " --> pdb=" O   ALA A 658 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 668 through 677
      removed outlier: 3.704A  pdb=" N   VAL A 672 " --> pdb=" O   TYR A 668 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   TRP A 677 " --> pdb=" O   LEU A 673 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 682 through 689
    Processing helix  chain 'A' and resid 692 through 710
      removed outlier: 3.531A  pdb=" N   ALA A 696 " --> pdb=" O   LEU A 692 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   GLY A 700 " --> pdb=" O   ALA A 696 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   GLN A 710 " --> pdb=" O   LEU A 706 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 729 through 735
    Processing helix  chain 'A' and resid 735 through 752
    Processing helix  chain 'A' and resid 753 through 755
      No H-bonds generated for 'chain 'A' and resid 753 through 755'
    Processing helix  chain 'A' and resid 848 through 854
    Processing helix  chain 'A' and resid 879 through 881
      No H-bonds generated for 'chain 'A' and resid 879 through 881'
    Processing helix  chain 'A' and resid 898 through 910
    Processing helix  chain 'A' and resid 916 through 927
      removed outlier: 4.324A  pdb=" N   ARG A 922 " --> pdb=" O   PRO A 918 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 944 through 952
      removed outlier: 4.027A  pdb=" N   LEU A 948 " --> pdb=" O   MET A 944 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   ILE A 952 " --> pdb=" O   LEU A 948 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 953 through 955
      No H-bonds generated for 'chain 'A' and resid 953 through 955'
    Processing helix  chain 'A' and resid 971 through 985
      removed outlier: 3.890A  pdb=" N   ARG A 976 " --> pdb=" O   PRO A 972 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   GLY A 977 " --> pdb=" O   ALA A 973 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1074 through 1086
      removed outlier: 3.745A  pdb=" N   LEU A1078 " --> pdb=" O   GLY A1074 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1109 through 1125
      removed outlier: 3.890A  pdb=" N   GLU A1119 " --> pdb=" O   THR A1115 " (cutoff:3.500A)
      removed outlier: 4.403A  pdb=" N   ALA A1125 " --> pdb=" O   ASP A1121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1138 through 1148
      removed outlier: 3.696A  pdb=" N   ILE A1142 " --> pdb=" O   SER A1138 " (cutoff:3.500A)
      removed outlier: 4.530A  pdb=" N   GLU A1148 " --> pdb=" O   LEU A1144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1215 through 1235
      removed outlier: 3.924A  pdb=" N   ARG A1234 " --> pdb=" O   LEU A1230 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   SER A1235 " --> pdb=" O   LEU A1231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1235 through 1257
      Proline residue:  A1246  - end of helix
      removed outlier: 3.877A  pdb=" N   GLY A1251 " --> pdb=" O   ALA A1247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1272 through 1277
      removed outlier: 3.632A  pdb=" N   MET A1275 " --> pdb=" O   SER A1272 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   GLY A1277 " --> pdb=" O   THR A1274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1290 through 1304
      removed outlier: 3.536A  pdb=" N   ALA A1294 " --> pdb=" O   ASP A1290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1310 through 1315
    Processing helix  chain 'A' and resid 1324 through 1334
      removed outlier: 3.985A  pdb=" N   VAL A1330 " --> pdb=" O   GLU A1326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1390 through 1400
      Proline residue:  A1396  - end of helix
      removed outlier: 3.597A  pdb=" N   VAL A1399 " --> pdb=" O   TYR A1395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1428 through 1443
    Processing helix  chain 'A' and resid 1449 through 1464
      removed outlier: 3.818A  pdb=" N   VAL A1454 " --> pdb=" O   ALA A1450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1465 through 1467
      No H-bonds generated for 'chain 'A' and resid 1465 through 1467'
    Processing helix  chain 'A' and resid 1481 through 1498
    Processing helix  chain 'A' and resid 1503 through 1508
    Processing helix  chain 'A' and resid 1520 through 1529
      removed outlier: 4.050A  pdb=" N   SER A1525 " --> pdb=" O   LYS A1521 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1533 through 1547
      removed outlier: 3.994A  pdb=" N   VAL A1543 " --> pdb=" O   SER A1539 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1550 through 1563
    Processing helix  chain 'A' and resid 1564 through 1571
      removed outlier: 3.550A  pdb=" N   LEU A1568 " --> pdb=" O   ARG A1564 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1575 through 1605
      removed outlier: 4.368A  pdb=" N   LEU A1585 " --> pdb=" O   LEU A1581 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   TRP A1586 " --> pdb=" O   GLY A1582 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   VAL A1593 " --> pdb=" O   CYS A1589 " (cutoff:3.500A)
      Proline residue:  A1594  - end of helix
      removed outlier: 3.813A  pdb=" N   ILE A1597 " --> pdb=" O   VAL A1593 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1615 through 1631
      removed outlier: 3.785A  pdb=" N   THR A1631 " --> pdb=" O   GLY A1627 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1632 through 1641
      removed outlier: 4.289A  pdb=" N   TYR A1635 " --> pdb=" O   PRO A1632 " (cutoff:3.500A)
      Proline residue:  A1636  - end of helix
      removed outlier: 3.748A  pdb=" N   PHE A1639 " --> pdb=" O   PRO A1636 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1643 through 1671
      removed outlier: 4.484A  pdb=" N   THR A1666 " --> pdb=" O   GLY A1662 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1675 through 1689
      removed outlier: 3.527A  pdb=" N   GLU A1679 " --> pdb=" O   GLN A1675 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   LEU A1689 " --> pdb=" O   LYS A1685 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1691 through 1714
    Processing helix  chain 'A' and resid 1730 through 1753
      removed outlier: 3.526A  pdb=" N   LEU A1734 " --> pdb=" O   VAL A1730 " (cutoff:3.500A)
      Proline residue:  A1742  - end of helix
      removed outlier: 3.830A  pdb=" N   THR A1748 " --> pdb=" O   PHE A1744 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   LEU A1749 " --> pdb=" O   LEU A1745 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1775 through 1786
      removed outlier: 4.002A  pdb=" N   ARG A1782 " --> pdb=" O   ARG A1778 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1833 through 1842
      removed outlier: 3.770A  pdb=" N   VAL A1840 " --> pdb=" O   THR A1836 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1862 through 1866
    Processing helix  chain 'A' and resid 1883 through 1895
    Processing helix  chain 'A' and resid 1898 through 1912
      removed outlier: 4.516A  pdb=" N   ALA A1903 " --> pdb=" O   GLU A1899 " (cutoff:3.500A)
      removed outlier: 4.507A  pdb=" N   GLN A1904 " --> pdb=" O   ALA A1900 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1922 through 1926
      removed outlier: 3.734A  pdb=" N   TYR A1926 " --> pdb=" O   ALA A1923 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1927 through 1941
    Processing helix  chain 'A' and resid 1957 through 1974
    Processing helix  chain 'A' and resid 1985 through 1992
      removed outlier: 3.861A  pdb=" N   GLU A1989 " --> pdb=" O   MET A1985 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2008 through 2017
    Processing helix  chain 'A' and resid 2030 through 2042
      removed outlier: 4.181A  pdb=" N   ALA A2034 " --> pdb=" O   ARG A2030 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   PHE A2037 " --> pdb=" O   PRO A2033 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2067 through 2078
      removed outlier: 3.774A  pdb=" N   GLY A2072 " --> pdb=" O   ALA A2068 " (cutoff:3.500A)
      removed outlier: 4.688A  pdb=" N   GLU A2073 " --> pdb=" O   ARG A2069 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2094 through 2103
      removed outlier: 3.884A  pdb=" N   LEU A2098 " --> pdb=" O   GLU A2094 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 50
    Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60
      removed outlier: 6.351A  pdb=" N   TYR A 528 " --> pdb=" O   ILE A1473 " (cutoff:3.500A)
      removed outlier: 6.980A  pdb=" N   PHE A1475 " --> pdb=" O   TYR A 528 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   GLN A 530 " --> pdb=" O   PHE A1475 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   SER A1418 " --> pdb=" O   LYS A1472 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 295 through 297
      removed outlier: 5.867A  pdb=" N   LEU A 295 " --> pdb=" O   GLU A 413 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 437 through 439
      removed outlier: 6.776A  pdb=" N   VAL A 462 " --> pdb=" O   THR A1511 " (cutoff:3.500A)
      removed outlier: 7.510A  pdb=" N   LEU A1513 " --> pdb=" O   VAL A 462 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   ILE A 464 " --> pdb=" O   LEU A1513 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 883 through 886
      removed outlier: 6.815A  pdb=" N   GLY A 884 " --> pdb=" O   ILE A 962 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   LEU A 993 " --> pdb=" O   THR A 837 " (cutoff:3.500A)
      removed outlier: 5.903A  pdb=" N   ILE A 836 " --> pdb=" O   ARG A1007 " (cutoff:3.500A)
      removed outlier: 7.445A  pdb=" N   ALA A1009 " --> pdb=" O   ILE A 836 " (cutoff:3.500A)
      removed outlier: 6.151A  pdb=" N   ALA A 838 " --> pdb=" O   ALA A1009 " (cutoff:3.500A)
      removed outlier: 7.551A  pdb=" N   VAL A1011 " --> pdb=" O   ALA A 838 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   LEU A 840 " --> pdb=" O   VAL A1011 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   CYS A1018 " --> pdb=" O   VAL A1010 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   ALA A1012 " --> pdb=" O   LEU A1016 " (cutoff:3.500A)
      removed outlier: 5.184A  pdb=" N   LEU A1016 " --> pdb=" O   ALA A1012 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1090 through 1095
      removed outlier: 6.802A  pdb=" N   VAL A1100 " --> pdb=" O   VAL A1092 " (cutoff:3.500A)
      removed outlier: 4.861A  pdb=" N   GLU A1094 " --> pdb=" O   GLU A1098 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   GLU A1098 " --> pdb=" O   GLU A1094 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1280 through 1282
      removed outlier: 6.710A  pdb=" N   SER A1281 " --> pdb=" O   GLN A1380 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1815 through 1817
      removed outlier: 3.627A  pdb=" N   LEU A1793 " --> pdb=" O   ILE A1817 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1869 through 1870
      removed outlier: 5.778A  pdb=" N   GLY A1870 " --> pdb=" O   PHE A1948 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   ASP A1950 " --> pdb=" O   GLY A1870 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   VAL A1947 " --> pdb=" O   MET A1979 " (cutoff:3.500A)
      removed outlier: 8.051A  pdb=" N   THR A1981 " --> pdb=" O   VAL A1947 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   LEU A1949 " --> pdb=" O   THR A1981 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   PHE A1823 " --> pdb=" O   VAL A1978 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   LEU A1980 " --> pdb=" O   PHE A1823 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   GLY A1824 " --> pdb=" O   ALA A1996 " (cutoff:3.500A)
      removed outlier: 7.787A  pdb=" N   MET A1998 " --> pdb=" O   GLY A1824 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   LEU A1826 " --> pdb=" O   MET A1998 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 2055 through 2058
      removed outlier: 3.717A  pdb=" N   LEU A2055 " --> pdb=" O   LEU A2024 " (cutoff:3.500A)

    689 hydrogen bonds defined for protein.
    2007 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: 6.47

  Time building geometry restraints manager: 4.21 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 4672
        1.35 -     1.47: 3547
        1.47 -     1.60: 6251
        1.60 -     1.73: 1
        1.73 -     1.86: 96
  Bond restraints: 14567
  Sorted by residual:
  bond pdb=" N   PRO A2060 "
       pdb=" CD  PRO A2060 "
    ideal  model  delta    sigma   weight residual
    1.473  1.531 -0.058 1.40e-02 5.10e+03 1.74e+01
  bond pdb=" CA  THR A1631 "
       pdb=" CB  THR A1631 "
    ideal  model  delta    sigma   weight residual
    1.531  1.585 -0.053 1.33e-02 5.65e+03 1.61e+01
  bond pdb=" CB  VAL A2038 "
       pdb=" CG1 VAL A2038 "
    ideal  model  delta    sigma   weight residual
    1.521  1.397  0.124 3.30e-02 9.18e+02 1.42e+01
  bond pdb=" CB  MET A1979 "
       pdb=" CG  MET A1979 "
    ideal  model  delta    sigma   weight residual
    1.520  1.632 -0.112 3.00e-02 1.11e+03 1.41e+01
  bond pdb=" N   PRO A1503 "
       pdb=" CD  PRO A1503 "
    ideal  model  delta    sigma   weight residual
    1.473  1.525 -0.052 1.40e-02 5.10e+03 1.40e+01
  ... (remaining 14562 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.69: 19683
        5.69 -    11.38: 121
       11.38 -    17.07: 7
       17.07 -    22.76: 0
       22.76 -    28.46: 1
  Bond angle restraints: 19812
  Sorted by residual:
  angle pdb=" CB  MET A1979 "
        pdb=" CG  MET A1979 "
        pdb=" SD  MET A1979 "
      ideal   model   delta    sigma   weight residual
     112.70  141.16  -28.46 3.00e+00 1.11e-01 9.00e+01
  angle pdb=" N   VAL A 898 "
        pdb=" CA  VAL A 898 "
        pdb=" C   VAL A 898 "
      ideal   model   delta    sigma   weight residual
     111.00  120.27   -9.27 1.09e+00 8.42e-01 7.23e+01
  angle pdb=" N   LEU A 506 "
        pdb=" CA  LEU A 506 "
        pdb=" C   LEU A 506 "
      ideal   model   delta    sigma   weight residual
     110.97  103.69    7.28 1.09e+00 8.42e-01 4.46e+01
  angle pdb=" C   THR A 897 "
        pdb=" CA  THR A 897 "
        pdb=" CB  THR A 897 "
      ideal   model   delta    sigma   weight residual
     110.42  122.52  -12.10 1.99e+00 2.53e-01 3.70e+01
  angle pdb=" N   LEU A  70 "
        pdb=" CA  LEU A  70 "
        pdb=" C   LEU A  70 "
      ideal   model   delta    sigma   weight residual
     110.97  104.47    6.50 1.09e+00 8.42e-01 3.55e+01
  ... (remaining 19807 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.08: 7429
       18.08 -    36.16: 935
       36.16 -    54.24: 262
       54.24 -    72.32: 31
       72.32 -    90.40: 16
  Dihedral angle restraints: 8673
    sinusoidal: 3422
      harmonic: 5251
  Sorted by residual:
  dihedral pdb=" CB  CYS A  54 "
           pdb=" SG  CYS A  54 "
           pdb=" SG  CYS A  81 "
           pdb=" CB  CYS A  81 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -176.60  -90.40     1      1.00e+01 1.00e-02 9.67e+01
  dihedral pdb=" CB  CYS A1017 "
           pdb=" SG  CYS A1017 "
           pdb=" SG  CYS A1150 "
           pdb=" CB  CYS A1150 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -157.24   71.24     1      1.00e+01 1.00e-02 6.51e+01
  dihedral pdb=" C   THR A 897 "
           pdb=" N   THR A 897 "
           pdb=" CA  THR A 897 "
           pdb=" CB  THR A 897 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -137.54   15.54     0      2.50e+00 1.60e-01 3.86e+01
  ... (remaining 8670 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.118: 2175
       0.118 -    0.237: 66
       0.237 -    0.355: 12
       0.355 -    0.473: 2
       0.473 -    0.591: 3
  Chirality restraints: 2258
  Sorted by residual:
  chirality pdb=" CG  LEU A1751 "
            pdb=" CB  LEU A1751 "
            pdb=" CD1 LEU A1751 "
            pdb=" CD2 LEU A1751 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.00   -0.59 2.00e-01 2.50e+01 8.74e+00
  chirality pdb=" CA  THR A 897 "
            pdb=" N   THR A 897 "
            pdb=" C   THR A 897 "
            pdb=" CB  THR A 897 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.02    0.50 2.00e-01 2.50e+01 6.30e+00
  chirality pdb=" CB  VAL A 891 "
            pdb=" CA  VAL A 891 "
            pdb=" CG1 VAL A 891 "
            pdb=" CG2 VAL A 891 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.14   -0.49 2.00e-01 2.50e+01 6.00e+00
  ... (remaining 2255 not shown)

  Planarity restraints: 2544
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 897 "    0.025 2.00e-02 2.50e+03   5.23e-02 2.74e+01
        pdb=" C   THR A 897 "   -0.090 2.00e-02 2.50e+03
        pdb=" O   THR A 897 "    0.035 2.00e-02 2.50e+03
        pdb=" N   VAL A 898 "    0.030 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A2059 "   -0.082 5.00e-02 4.00e+02   1.21e-01 2.35e+01
        pdb=" N   PRO A2060 "    0.209 5.00e-02 4.00e+02
        pdb=" CA  PRO A2060 "   -0.065 5.00e-02 4.00e+02
        pdb=" CD  PRO A2060 "   -0.062 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A 574 "   -0.017 2.00e-02 2.50e+03   3.55e-02 1.26e+01
        pdb=" CD  GLU A 574 "    0.061 2.00e-02 2.50e+03
        pdb=" OE1 GLU A 574 "   -0.022 2.00e-02 2.50e+03
        pdb=" OE2 GLU A 574 "   -0.022 2.00e-02 2.50e+03
  ... (remaining 2541 not shown)

  Histogram of nonbonded interaction distances:
        1.68 -     2.32: 19
        2.32 -     2.97: 6264
        2.97 -     3.61: 22215
        3.61 -     4.26: 31787
        4.26 -     4.90: 51921
  Nonbonded interactions: 112206
  Sorted by model distance:
  nonbonded pdb=" CD2 PHE A2042 "
            pdb=" CD1 LEU A2059 "
     model   vdw
     1.678 3.760
  nonbonded pdb=" CG  PHE A2042 "
            pdb=" CD1 LEU A2059 "
     model   vdw
     2.190 3.680
  nonbonded pdb=" OG1 THR A2021 "
            pdb=" O   SER A2089 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" OG  SER A1984 "
            pdb=" OE1 GLU A1986 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" O   ARG A 334 "
            pdb=" OG1 THR A 337 "
     model   vdw
     2.247 3.040
  ... (remaining 112201 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.260
  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:          0.560
  Check model and map are aligned:         0.110
  Set scattering table:                    0.160
  Process input model:                     36.680
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7372
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   0.124  14572  Z= 0.251
  Angle     :  1.076  28.456  19822  Z= 0.542
  Chirality :  0.059   0.591   2258
  Planarity :  0.008   0.125   2544
  Dihedral  : 17.142  89.904   5280
  Min Nonbonded Distance : 1.678

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 29.90 %
    Favored  : 70.10 %
  Cbeta Deviations :  0.12 %
  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: -2.66 (0.18), residues: 1826
  helix: -1.20 (0.16), residues: 940
  sheet: -2.11 (0.35), residues: 199
  loop : -2.29 (0.22), residues: 687

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.002   TRP A1965 
 HIS   0.012   0.001   HIS A1887 
 PHE   0.045   0.003   PHE A1963 
 TYR   0.041   0.002   TYR A1591 
 ARG   0.027   0.001   ARG A 880 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14434 (  689)
  hydrogen bonds       : angle       6.93585 ( 2007)
  SS BOND              : bond        0.00330 (    5)
  SS BOND              : angle       0.77425 (   10)
  covalent geometry    : bond        0.00544 (14567)
  covalent geometry    : angle       1.07641 (19812)

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

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

  3652 Ramachandran restraints generated.
    1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3652 Ramachandran restraints generated.
    1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 1.535 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1571 MET cc_start: 0.8070 (mmp) cc_final: 0.7851 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 152
  average time/residue: 0.2267
  time to fit residues: 54.8464
Evaluate side-chains
  147 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 1.556 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 155 optimal weight:    7.9990
   chunk 139 optimal weight:    2.9990
   chunk 77 optimal weight:    0.0970
   chunk 47 optimal weight:    2.9990
   chunk 94 optimal weight:   20.0000
   chunk 74 optimal weight:    1.9990
   chunk 144 optimal weight:    5.9990
   chunk 55 optimal weight:    0.5980
   chunk 87 optimal weight:    3.9990
   chunk 107 optimal weight:    3.9990
   chunk 167 optimal weight:    6.9990
   overall best weight:    1.7384

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

Flipped N/Q/H residues before XYZ refinement:
** A1752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.152156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.121161 restraints weight = 37439.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.117605 restraints weight = 29141.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.118705 restraints weight = 23805.983|
|-----------------------------------------------------------------------------|
r_work (final): 0.3871
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7447
moved from start:          0.0897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  14572  Z= 0.164
  Angle     :  0.674  11.822  19822  Z= 0.333
  Chirality :  0.042   0.222   2258
  Planarity :  0.005   0.072   2544
  Dihedral  :  5.128  26.777   2004
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 26.45 %
    Favored  : 69.97 %
  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: -1.91 (0.19), residues: 1826
  helix: -0.38 (0.17), residues: 958
  sheet: -1.98 (0.36), residues: 204
  loop : -2.24 (0.23), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP A1965 
 HIS   0.005   0.001   HIS A1887 
 PHE   0.028   0.002   PHE A1963 
 TYR   0.021   0.001   TYR A1591 
 ARG   0.006   0.000   ARG A 880 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03981 (  689)
  hydrogen bonds       : angle       5.21424 ( 2007)
  SS BOND              : bond        0.00266 (    5)
  SS BOND              : angle       0.52945 (   10)
  covalent geometry    : bond        0.00361 (14567)
  covalent geometry    : angle       0.67408 (19812)

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

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

  3652 Ramachandran restraints generated.
    1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3652 Ramachandran restraints generated.
    1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 163
  time to evaluate  : 1.652 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 MET cc_start: 0.9136 (mmm) cc_final: 0.8851 (tpp)
REVERT: A  967 THR cc_start: 0.7873 (OUTLIER) cc_final: 0.7554 (m)
REVERT: A  998 LEU cc_start: 0.8822 (mt) cc_final: 0.8605 (mt)
REVERT: A 1839 MET cc_start: 0.5710 (pmm) cc_final: 0.5510 (pmm)
  outliers start: 54
  outliers final: 30
  residues processed: 203
  average time/residue: 0.2503
  time to fit residues: 80.6353
Evaluate side-chains
  176 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 145
  time to evaluate  : 1.966 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   38 ILE
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  225 CYS
Chi-restraints excluded: chain A residue  431 GLU
Chi-restraints excluded: chain A residue  564 LEU
Chi-restraints excluded: chain A residue  593 LEU
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  641 THR
Chi-restraints excluded: chain A residue  672 VAL
Chi-restraints excluded: chain A residue  809 VAL
Chi-restraints excluded: chain A residue  812 LEU
Chi-restraints excluded: chain A residue  902 VAL
Chi-restraints excluded: chain A residue  967 THR
Chi-restraints excluded: chain A residue  983 LEU
Chi-restraints excluded: chain A residue 1004 LEU
Chi-restraints excluded: chain A residue 1021 SER
Chi-restraints excluded: chain A residue 1075 THR
Chi-restraints excluded: chain A residue 1092 VAL
Chi-restraints excluded: chain A residue 1143 PHE
Chi-restraints excluded: chain A residue 1284 SER
Chi-restraints excluded: chain A residue 1323 VAL
Chi-restraints excluded: chain A residue 1621 LEU
Chi-restraints excluded: chain A residue 1634 MET
Chi-restraints excluded: chain A residue 1643 VAL
Chi-restraints excluded: chain A residue 1693 HIS
Chi-restraints excluded: chain A residue 1965 TRP
Chi-restraints excluded: chain A residue 2020 HIS
Chi-restraints excluded: chain A residue 2026 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 118 optimal weight:    9.9990
   chunk 73 optimal weight:    4.9990
   chunk 20 optimal weight:    5.9990
   chunk 151 optimal weight:    9.9990
   chunk 60 optimal weight:    0.0370
   chunk 17 optimal weight:    4.9990
   chunk 13 optimal weight:   30.0000
   chunk 1 optimal weight:    3.9990
   chunk 78 optimal weight:    3.9990
   chunk 101 optimal weight:    0.6980
   chunk 22 optimal weight:    0.7980
   overall best weight:    1.9062

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

Flipped N/Q/H residues before XYZ refinement:
A 624 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.151169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.118653 restraints weight = 37441.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.114039 restraints weight = 26242.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.115190 restraints weight = 21906.612|
|-----------------------------------------------------------------------------|
r_work (final): 0.3809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
moved from start:          0.1209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  14572  Z= 0.165
  Angle     :  0.675  11.382  19822  Z= 0.327
  Chirality :  0.042   0.220   2258
  Planarity :  0.005   0.064   2544
  Dihedral  :  4.961  27.255   2004
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 26.91 %
    Favored  : 68.84 %
  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: -1.57 (0.20), residues: 1826
  helix: -0.02 (0.17), residues: 954
  sheet: -1.96 (0.36), residues: 202
  loop : -2.16 (0.23), residues: 670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.001   TRP A1965 
 HIS   0.009   0.001   HIS A1887 
 PHE   0.046   0.002   PHE A1584 
 TYR   0.019   0.001   TYR A1591 
 ARG   0.005   0.000   ARG A 880 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03684 (  689)
  hydrogen bonds       : angle       4.99533 ( 2007)
  SS BOND              : bond        0.00236 (    5)
  SS BOND              : angle       0.51166 (   10)
  covalent geometry    : bond        0.00372 (14567)
  covalent geometry    : angle       0.67471 (19812)

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

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

  3652 Ramachandran restraints generated.
    1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3652 Ramachandran restraints generated.
    1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 169
  time to evaluate  : 1.937 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 MET cc_start: 0.9152 (mmm) cc_final: 0.8838 (tpp)
REVERT: A  192 GLN cc_start: 0.8173 (mm-40) cc_final: 0.7674 (pp30)
REVERT: A  577 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8849 (pp)
REVERT: A  870 HIS cc_start: 0.6694 (OUTLIER) cc_final: 0.6459 (p-80)
REVERT: A  967 THR cc_start: 0.7948 (OUTLIER) cc_final: 0.7589 (m)
REVERT: A 1590 ASN cc_start: 0.8340 (t0) cc_final: 0.8032 (t0)
REVERT: A 1703 MET cc_start: 0.8739 (ppp) cc_final: 0.8474 (ppp)
REVERT: A 1879 PHE cc_start: 0.8947 (m-80) cc_final: 0.8536 (m-10)
REVERT: A 1979 MET cc_start: 0.7094 (mmm) cc_final: 0.6174 (mmm)
  outliers start: 64
  outliers final: 35
  residues processed: 217
  average time/residue: 0.2336
  time to fit residues: 83.0283
Evaluate side-chains
  189 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 151
  time to evaluate  : 1.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   38 ILE
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  225 CYS
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  431 GLU
Chi-restraints excluded: chain A residue  577 LEU
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  593 LEU
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  672 VAL
Chi-restraints excluded: chain A residue  727 VAL
Chi-restraints excluded: chain A residue  809 VAL
Chi-restraints excluded: chain A residue  870 HIS
Chi-restraints excluded: chain A residue  902 VAL
Chi-restraints excluded: chain A residue  967 THR
Chi-restraints excluded: chain A residue  983 LEU
Chi-restraints excluded: chain A residue 1004 LEU
Chi-restraints excluded: chain A residue 1092 VAL
Chi-restraints excluded: chain A residue 1121 ASP
Chi-restraints excluded: chain A residue 1138 SER
Chi-restraints excluded: chain A residue 1143 PHE
Chi-restraints excluded: chain A residue 1284 SER
Chi-restraints excluded: chain A residue 1323 VAL
Chi-restraints excluded: chain A residue 1586 TRP
Chi-restraints excluded: chain A residue 1634 MET
Chi-restraints excluded: chain A residue 1643 VAL
Chi-restraints excluded: chain A residue 1693 HIS
Chi-restraints excluded: chain A residue 1701 ILE
Chi-restraints excluded: chain A residue 1841 THR
Chi-restraints excluded: chain A residue 1868 SER
Chi-restraints excluded: chain A residue 1881 LEU
Chi-restraints excluded: chain A residue 1965 TRP
Chi-restraints excluded: chain A residue 2020 HIS
Chi-restraints excluded: chain A residue 2026 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 183 optimal weight:    5.9990
   chunk 14 optimal weight:    3.9990
   chunk 71 optimal weight:    9.9990
   chunk 121 optimal weight:    1.9990
   chunk 135 optimal weight:    4.9990
   chunk 139 optimal weight:   10.0000
   chunk 41 optimal weight:    2.9990
   chunk 104 optimal weight:    0.9990
   chunk 140 optimal weight:    1.9990
   chunk 168 optimal weight:    0.5980
   chunk 51 optimal weight:    0.8980
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
A1606 GLN
** A1752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.151926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.121316 restraints weight = 37333.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.117440 restraints weight = 29156.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.118367 restraints weight = 24221.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.3863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7467
moved from start:          0.1399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  14572  Z= 0.133
  Angle     :  0.655  11.457  19822  Z= 0.314
  Chirality :  0.042   0.240   2258
  Planarity :  0.004   0.062   2544
  Dihedral  :  4.790  28.439   2004
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 26.78 %
    Favored  : 69.10 %
  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: -1.30 (0.20), residues: 1826
  helix:  0.24 (0.17), residues: 950
  sheet: -1.84 (0.37), residues: 202
  loop : -2.09 (0.23), residues: 674

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.001   TRP A1965 
 HIS   0.010   0.001   HIS A1887 
 PHE   0.032   0.002   PHE A1584 
 TYR   0.018   0.001   TYR A1591 
 ARG   0.006   0.000   ARG A 880 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03359 (  689)
  hydrogen bonds       : angle       4.83631 ( 2007)
  SS BOND              : bond        0.00204 (    5)
  SS BOND              : angle       0.57076 (   10)
  covalent geometry    : bond        0.00301 (14567)
  covalent geometry    : angle       0.65553 (19812)

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

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

  3652 Ramachandran restraints generated.
    1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3652 Ramachandran restraints generated.
    1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 165
  time to evaluate  : 1.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 MET cc_start: 0.9142 (mmm) cc_final: 0.8834 (tpp)
REVERT: A  192 GLN cc_start: 0.8034 (mm-40) cc_final: 0.7686 (pp30)
REVERT: A  295 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8452 (mp)
REVERT: A  577 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8783 (pp)
REVERT: A  870 HIS cc_start: 0.6635 (OUTLIER) cc_final: 0.6383 (p-80)
REVERT: A  967 THR cc_start: 0.7854 (OUTLIER) cc_final: 0.7474 (m)
REVERT: A 1590 ASN cc_start: 0.8125 (t0) cc_final: 0.7863 (t0)
REVERT: A 1879 PHE cc_start: 0.8688 (m-80) cc_final: 0.8301 (m-10)
REVERT: A 1979 MET cc_start: 0.7113 (mmm) cc_final: 0.6303 (mmm)
  outliers start: 62
  outliers final: 46
  residues processed: 212
  average time/residue: 0.2066
  time to fit residues: 70.9103
Evaluate side-chains
  203 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 153
  time to evaluate  : 1.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   37 PHE
Chi-restraints excluded: chain A residue   38 ILE
Chi-restraints excluded: chain A residue   54 CYS
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  431 GLU
Chi-restraints excluded: chain A residue  564 LEU
Chi-restraints excluded: chain A residue  577 LEU
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain A residue  593 LEU
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  672 VAL
Chi-restraints excluded: chain A residue  754 VAL
Chi-restraints excluded: chain A residue  809 VAL
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  870 HIS
Chi-restraints excluded: chain A residue  923 LEU
Chi-restraints excluded: chain A residue  967 THR
Chi-restraints excluded: chain A residue  983 LEU
Chi-restraints excluded: chain A residue 1004 LEU
Chi-restraints excluded: chain A residue 1075 THR
Chi-restraints excluded: chain A residue 1092 VAL
Chi-restraints excluded: chain A residue 1099 LEU
Chi-restraints excluded: chain A residue 1121 ASP
Chi-restraints excluded: chain A residue 1138 SER
Chi-restraints excluded: chain A residue 1143 PHE
Chi-restraints excluded: chain A residue 1284 SER
Chi-restraints excluded: chain A residue 1323 VAL
Chi-restraints excluded: chain A residue 1458 LEU
Chi-restraints excluded: chain A residue 1586 TRP
Chi-restraints excluded: chain A residue 1634 MET
Chi-restraints excluded: chain A residue 1643 VAL
Chi-restraints excluded: chain A residue 1693 HIS
Chi-restraints excluded: chain A residue 1701 ILE
Chi-restraints excluded: chain A residue 1749 LEU
Chi-restraints excluded: chain A residue 1841 THR
Chi-restraints excluded: chain A residue 1868 SER
Chi-restraints excluded: chain A residue 1881 LEU
Chi-restraints excluded: chain A residue 1946 VAL
Chi-restraints excluded: chain A residue 1964 LEU
Chi-restraints excluded: chain A residue 1965 TRP
Chi-restraints excluded: chain A residue 1999 VAL
Chi-restraints excluded: chain A residue 2020 HIS
Chi-restraints excluded: chain A residue 2026 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 122 optimal weight:    0.5980
   chunk 176 optimal weight:    9.9990
   chunk 79 optimal weight:    5.9990
   chunk 157 optimal weight:    5.9990
   chunk 21 optimal weight:    4.9990
   chunk 63 optimal weight:    3.9990
   chunk 10 optimal weight:    4.9990
   chunk 106 optimal weight:    8.9990
   chunk 169 optimal weight:    8.9990
   chunk 144 optimal weight:    3.9990
   chunk 20 optimal weight:    7.9990
   overall best weight:    3.7188

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

Flipped N/Q/H residues before XYZ refinement:
** A1752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.148071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.117035 restraints weight = 37630.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.112941 restraints weight = 40314.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.114380 restraints weight = 40003.868|
|-----------------------------------------------------------------------------|
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7508
moved from start:          0.1766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056  14572  Z= 0.274
  Angle     :  0.745  11.277  19822  Z= 0.365
  Chirality :  0.045   0.257   2258
  Planarity :  0.005   0.059   2544
  Dihedral  :  5.029  29.011   2004
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 13.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  5.65 %
    Allowed  : 26.51 %
    Favored  : 67.84 %
  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: -1.45 (0.20), residues: 1826
  helix:  0.11 (0.17), residues: 961
  sheet: -2.02 (0.37), residues: 196
  loop : -2.14 (0.24), residues: 669

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A1965 
 HIS   0.010   0.001   HIS A1887 
 PHE   0.033   0.002   PHE A1584 
 TYR   0.019   0.002   TYR A 560 
 ARG   0.006   0.000   ARG A 880 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03738 (  689)
  hydrogen bonds       : angle       5.03486 ( 2007)
  SS BOND              : bond        0.00302 (    5)
  SS BOND              : angle       0.77416 (   10)
  covalent geometry    : bond        0.00619 (14567)
  covalent geometry    : angle       0.74532 (19812)

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

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

  3652 Ramachandran restraints generated.
    1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3652 Ramachandran restraints generated.
    1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 85
    poor density    : 152
  time to evaluate  : 1.398 
Fit side-chains
   revert: symmetry clash
REVERT: A   16 MET cc_start: 0.9089 (mmm) cc_final: 0.8774 (tpp)
REVERT: A  192 GLN cc_start: 0.7872 (mm-40) cc_final: 0.7602 (pp30)
REVERT: A  577 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8784 (pp)
REVERT: A  746 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7781 (tt)
REVERT: A  870 HIS cc_start: 0.6910 (OUTLIER) cc_final: 0.6652 (p-80)
REVERT: A  880 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.6974 (mmm-85)
REVERT: A  967 THR cc_start: 0.7784 (OUTLIER) cc_final: 0.7437 (m)
REVERT: A 1590 ASN cc_start: 0.7963 (t0) cc_final: 0.7728 (t0)
REVERT: A 1868 SER cc_start: 0.3589 (OUTLIER) cc_final: 0.3377 (m)
REVERT: A 1879 PHE cc_start: 0.8513 (m-80) cc_final: 0.8202 (m-10)
  outliers start: 85
  outliers final: 55
  residues processed: 219
  average time/residue: 0.2243
  time to fit residues: 77.6932
Evaluate side-chains
  211 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 150
  time to evaluate  : 1.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   38 ILE
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue   44 HIS
Chi-restraints excluded: chain A residue   54 CYS
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  225 CYS
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  577 LEU
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain A residue  641 THR
Chi-restraints excluded: chain A residue  672 VAL
Chi-restraints excluded: chain A residue  719 VAL
Chi-restraints excluded: chain A residue  727 VAL
Chi-restraints excluded: chain A residue  746 LEU
Chi-restraints excluded: chain A residue  754 VAL
Chi-restraints excluded: chain A residue  809 VAL
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  870 HIS
Chi-restraints excluded: chain A residue  880 ARG
Chi-restraints excluded: chain A residue  896 LEU
Chi-restraints excluded: chain A residue  902 VAL
Chi-restraints excluded: chain A residue  923 LEU
Chi-restraints excluded: chain A residue  967 THR
Chi-restraints excluded: chain A residue  983 LEU
Chi-restraints excluded: chain A residue  995 THR
Chi-restraints excluded: chain A residue 1004 LEU
Chi-restraints excluded: chain A residue 1075 THR
Chi-restraints excluded: chain A residue 1092 VAL
Chi-restraints excluded: chain A residue 1099 LEU
Chi-restraints excluded: chain A residue 1121 ASP
Chi-restraints excluded: chain A residue 1138 SER
Chi-restraints excluded: chain A residue 1143 PHE
Chi-restraints excluded: chain A residue 1284 SER
Chi-restraints excluded: chain A residue 1300 LEU
Chi-restraints excluded: chain A residue 1323 VAL
Chi-restraints excluded: chain A residue 1455 LEU
Chi-restraints excluded: chain A residue 1458 LEU
Chi-restraints excluded: chain A residue 1470 SER
Chi-restraints excluded: chain A residue 1487 VAL
Chi-restraints excluded: chain A residue 1569 GLN
Chi-restraints excluded: chain A residue 1586 TRP
Chi-restraints excluded: chain A residue 1621 LEU
Chi-restraints excluded: chain A residue 1643 VAL
Chi-restraints excluded: chain A residue 1693 HIS
Chi-restraints excluded: chain A residue 1701 ILE
Chi-restraints excluded: chain A residue 1749 LEU
Chi-restraints excluded: chain A residue 1841 THR
Chi-restraints excluded: chain A residue 1868 SER
Chi-restraints excluded: chain A residue 1946 VAL
Chi-restraints excluded: chain A residue 1964 LEU
Chi-restraints excluded: chain A residue 1965 TRP
Chi-restraints excluded: chain A residue 1999 VAL
Chi-restraints excluded: chain A residue 2026 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 95 optimal weight:    7.9990
   chunk 76 optimal weight:    0.1980
   chunk 144 optimal weight:    7.9990
   chunk 46 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 163 optimal weight:    6.9990
   chunk 23 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0370
   chunk 114 optimal weight:    0.8980
   chunk 182 optimal weight:   10.0000
   chunk 13 optimal weight:   20.0000
   overall best weight:    0.5860

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

Flipped N/Q/H residues before XYZ refinement:
A 507 GLN
A 945 GLN
A1752 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.152248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.120998 restraints weight = 37356.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.117590 restraints weight = 29642.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.118453 restraints weight = 22767.731|
|-----------------------------------------------------------------------------|
r_work (final): 0.3862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7460
moved from start:          0.1778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  14572  Z= 0.118
  Angle     :  0.681  12.324  19822  Z= 0.322
  Chirality :  0.042   0.249   2258
  Planarity :  0.004   0.059   2544
  Dihedral  :  4.702  27.044   2004
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 28.17 %
    Favored  : 67.77 %
  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: -1.13 (0.20), residues: 1826
  helix:  0.41 (0.17), residues: 951
  sheet: -2.00 (0.36), residues: 204
  loop : -1.96 (0.24), residues: 671

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.001   TRP A1965 
 HIS   0.010   0.001   HIS A1887 
 PHE   0.038   0.001   PHE A1584 
 TYR   0.021   0.001   TYR A1591 
 ARG   0.005   0.000   ARG A 880 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03243 (  689)
  hydrogen bonds       : angle       4.76115 ( 2007)
  SS BOND              : bond        0.00232 (    5)
  SS BOND              : angle       0.55427 (   10)
  covalent geometry    : bond        0.00266 (14567)
  covalent geometry    : angle       0.68154 (19812)

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

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

  3652 Ramachandran restraints generated.
    1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3652 Ramachandran restraints generated.
    1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 165
  time to evaluate  : 1.607 
Fit side-chains
REVERT: A   16 MET cc_start: 0.9079 (mmm) cc_final: 0.8764 (tpp)
REVERT: A  192 GLN cc_start: 0.8093 (mm-40) cc_final: 0.7716 (pp30)
REVERT: A  511 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7688 (mm-30)
REVERT: A  577 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8734 (pp)
REVERT: A  870 HIS cc_start: 0.6782 (OUTLIER) cc_final: 0.6530 (p-80)
REVERT: A  944 MET cc_start: 0.7538 (tmm) cc_final: 0.7079 (tmm)
REVERT: A  967 THR cc_start: 0.7816 (OUTLIER) cc_final: 0.7406 (m)
REVERT: A 1590 ASN cc_start: 0.8175 (t0) cc_final: 0.7894 (t0)
REVERT: A 1879 PHE cc_start: 0.8774 (m-80) cc_final: 0.8407 (m-10)
REVERT: A 1979 MET cc_start: 0.6186 (mmm) cc_final: 0.5696 (mmm)
  outliers start: 61
  outliers final: 43
  residues processed: 211
  average time/residue: 0.2076
  time to fit residues: 70.9625
Evaluate side-chains
  201 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 155
  time to evaluate  : 1.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   37 PHE
Chi-restraints excluded: chain A residue   38 ILE
Chi-restraints excluded: chain A residue   54 CYS
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  577 LEU
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  593 LEU
Chi-restraints excluded: chain A residue  604 LEU
Chi-restraints excluded: chain A residue  727 VAL
Chi-restraints excluded: chain A residue  754 VAL
Chi-restraints excluded: chain A residue  809 VAL
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  870 HIS
Chi-restraints excluded: chain A residue  923 LEU
Chi-restraints excluded: chain A residue  967 THR
Chi-restraints excluded: chain A residue  995 THR
Chi-restraints excluded: chain A residue 1004 LEU
Chi-restraints excluded: chain A residue 1075 THR
Chi-restraints excluded: chain A residue 1092 VAL
Chi-restraints excluded: chain A residue 1099 LEU
Chi-restraints excluded: chain A residue 1121 ASP
Chi-restraints excluded: chain A residue 1138 SER
Chi-restraints excluded: chain A residue 1143 PHE
Chi-restraints excluded: chain A residue 1284 SER
Chi-restraints excluded: chain A residue 1323 VAL
Chi-restraints excluded: chain A residue 1455 LEU
Chi-restraints excluded: chain A residue 1458 LEU
Chi-restraints excluded: chain A residue 1569 GLN
Chi-restraints excluded: chain A residue 1586 TRP
Chi-restraints excluded: chain A residue 1621 LEU
Chi-restraints excluded: chain A residue 1643 VAL
Chi-restraints excluded: chain A residue 1693 HIS
Chi-restraints excluded: chain A residue 1701 ILE
Chi-restraints excluded: chain A residue 1735 LEU
Chi-restraints excluded: chain A residue 1841 THR
Chi-restraints excluded: chain A residue 1881 LEU
Chi-restraints excluded: chain A residue 1946 VAL
Chi-restraints excluded: chain A residue 1965 TRP
Chi-restraints excluded: chain A residue 1988 CYS
Chi-restraints excluded: chain A residue 1999 VAL
Chi-restraints excluded: chain A residue 2020 HIS
Chi-restraints excluded: chain A residue 2026 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 106 optimal weight:    2.9990
   chunk 102 optimal weight:    2.9990
   chunk 100 optimal weight:    2.9990
   chunk 178 optimal weight:    0.0040
   chunk 85 optimal weight:    2.9990
   chunk 170 optimal weight:    9.9990
   chunk 94 optimal weight:    5.9990
   chunk 99 optimal weight:    7.9990
   chunk 7 optimal weight:    0.8980
   chunk 59 optimal weight:    7.9990
   chunk 172 optimal weight:    9.9990
   overall best weight:    1.9798

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

Flipped N/Q/H residues before XYZ refinement:
A 945 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.150516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.119357 restraints weight = 37585.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.116061 restraints weight = 29627.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.116541 restraints weight = 23105.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.3824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
moved from start:          0.1914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  14572  Z= 0.165
  Angle     :  0.696  12.399  19822  Z= 0.332
  Chirality :  0.042   0.274   2258
  Planarity :  0.004   0.058   2544
  Dihedral  :  4.700  27.438   2004
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 11.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 28.50 %
    Favored  : 66.91 %
  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: -1.10 (0.20), residues: 1826
  helix:  0.40 (0.17), residues: 953
  sheet: -1.92 (0.37), residues: 193
  loop : -1.95 (0.24), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP A1965 
 HIS   0.011   0.001   HIS A1887 
 PHE   0.026   0.002   PHE A1584 
 TYR   0.018   0.001   TYR A 560 
 ARG   0.006   0.000   ARG A2002 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03255 (  689)
  hydrogen bonds       : angle       4.77102 ( 2007)
  SS BOND              : bond        0.00275 (    5)
  SS BOND              : angle       0.63008 (   10)
  covalent geometry    : bond        0.00378 (14567)
  covalent geometry    : angle       0.69560 (19812)

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

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

  3652 Ramachandran restraints generated.
    1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3652 Ramachandran restraints generated.
    1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 158
  time to evaluate  : 1.478 
Fit side-chains
   revert: symmetry clash
REVERT: A   16 MET cc_start: 0.9125 (mmm) cc_final: 0.8806 (tpp)
REVERT: A   89 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7426 (mm-30)
REVERT: A  192 GLN cc_start: 0.8108 (mm-40) cc_final: 0.7701 (pp30)
REVERT: A  577 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8771 (pp)
REVERT: A  588 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7758 (mtm-85)
REVERT: A  708 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.6937 (tt0)
REVERT: A  870 HIS cc_start: 0.6895 (OUTLIER) cc_final: 0.6598 (p-80)
REVERT: A  880 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.6986 (mmm-85)
REVERT: A  944 MET cc_start: 0.7515 (tmm) cc_final: 0.7000 (tmm)
REVERT: A  967 THR cc_start: 0.7853 (OUTLIER) cc_final: 0.7458 (m)
REVERT: A 1590 ASN cc_start: 0.8256 (t0) cc_final: 0.7986 (t0)
REVERT: A 1635 TYR cc_start: 0.7813 (m-80) cc_final: 0.7560 (m-80)
REVERT: A 1879 PHE cc_start: 0.8820 (m-80) cc_final: 0.8522 (m-10)
REVERT: A 1979 MET cc_start: 0.6475 (mmm) cc_final: 0.5950 (mmm)
REVERT: A 2056 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.7063 (ptm-80)
  outliers start: 69
  outliers final: 50
  residues processed: 211
  average time/residue: 0.2263
  time to fit residues: 75.2348
Evaluate side-chains
  215 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 157
  time to evaluate  : 1.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   38 ILE
Chi-restraints excluded: chain A residue   44 HIS
Chi-restraints excluded: chain A residue   54 CYS
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   89 GLU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  225 CYS
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  506 LEU
Chi-restraints excluded: chain A residue  577 LEU
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  588 ARG
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain A residue  593 LEU
Chi-restraints excluded: chain A residue  604 LEU
Chi-restraints excluded: chain A residue  637 VAL
Chi-restraints excluded: chain A residue  672 VAL
Chi-restraints excluded: chain A residue  708 GLU
Chi-restraints excluded: chain A residue  727 VAL
Chi-restraints excluded: chain A residue  754 VAL
Chi-restraints excluded: chain A residue  809 VAL
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  870 HIS
Chi-restraints excluded: chain A residue  880 ARG
Chi-restraints excluded: chain A residue  923 LEU
Chi-restraints excluded: chain A residue  967 THR
Chi-restraints excluded: chain A residue  995 THR
Chi-restraints excluded: chain A residue 1004 LEU
Chi-restraints excluded: chain A residue 1075 THR
Chi-restraints excluded: chain A residue 1092 VAL
Chi-restraints excluded: chain A residue 1099 LEU
Chi-restraints excluded: chain A residue 1121 ASP
Chi-restraints excluded: chain A residue 1138 SER
Chi-restraints excluded: chain A residue 1143 PHE
Chi-restraints excluded: chain A residue 1284 SER
Chi-restraints excluded: chain A residue 1323 VAL
Chi-restraints excluded: chain A residue 1455 LEU
Chi-restraints excluded: chain A residue 1458 LEU
Chi-restraints excluded: chain A residue 1569 GLN
Chi-restraints excluded: chain A residue 1586 TRP
Chi-restraints excluded: chain A residue 1643 VAL
Chi-restraints excluded: chain A residue 1693 HIS
Chi-restraints excluded: chain A residue 1701 ILE
Chi-restraints excluded: chain A residue 1749 LEU
Chi-restraints excluded: chain A residue 1841 THR
Chi-restraints excluded: chain A residue 1868 SER
Chi-restraints excluded: chain A residue 1881 LEU
Chi-restraints excluded: chain A residue 1946 VAL
Chi-restraints excluded: chain A residue 1964 LEU
Chi-restraints excluded: chain A residue 1965 TRP
Chi-restraints excluded: chain A residue 1988 CYS
Chi-restraints excluded: chain A residue 1999 VAL
Chi-restraints excluded: chain A residue 2020 HIS
Chi-restraints excluded: chain A residue 2026 VAL
Chi-restraints excluded: chain A residue 2056 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 77 optimal weight:   10.0000
   chunk 34 optimal weight:    0.9990
   chunk 36 optimal weight:    0.8980
   chunk 57 optimal weight:    0.0970
   chunk 109 optimal weight:    6.9990
   chunk 70 optimal weight:    0.3980
   chunk 37 optimal weight:    1.9990
   chunk 182 optimal weight:   20.0000
   chunk 26 optimal weight:    3.9990
   chunk 143 optimal weight:    0.9980
   chunk 8 optimal weight:    0.4980
   overall best weight:    0.5778

-------------------------------------------------------------------------------
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 = 0.4376 r_free = 0.4376 target = 0.152602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.120727 restraints weight = 37381.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.117655 restraints weight = 25468.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.118289 restraints weight = 23413.941|
|-----------------------------------------------------------------------------|
r_work (final): 0.3865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
moved from start:          0.1951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  14572  Z= 0.111
  Angle     :  0.680  12.820  19822  Z= 0.318
  Chirality :  0.041   0.265   2258
  Planarity :  0.004   0.059   2544
  Dihedral  :  4.527  25.800   2004
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 29.24 %
    Favored  : 67.11 %
  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: -0.95 (0.20), residues: 1826
  helix:  0.55 (0.18), residues: 953
  sheet: -1.88 (0.37), residues: 200
  loop : -1.91 (0.24), residues: 673

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.001   TRP A1965 
 HIS   0.012   0.001   HIS A1887 
 PHE   0.028   0.001   PHE A1584 
 TYR   0.018   0.001   TYR A1591 
 ARG   0.005   0.000   ARG A 880 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03048 (  689)
  hydrogen bonds       : angle       4.64492 ( 2007)
  SS BOND              : bond        0.00247 (    5)
  SS BOND              : angle       0.53484 (   10)
  covalent geometry    : bond        0.00251 (14567)
  covalent geometry    : angle       0.67958 (19812)

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

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

  3652 Ramachandran restraints generated.
    1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3652 Ramachandran restraints generated.
    1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 166
  time to evaluate  : 1.423 
Fit side-chains
   revert: symmetry clash
REVERT: A   16 MET cc_start: 0.9071 (mmm) cc_final: 0.8750 (tpp)
REVERT: A  192 GLN cc_start: 0.8021 (mm-40) cc_final: 0.7701 (pp30)
REVERT: A  577 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8745 (pp)
REVERT: A  708 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6651 (tt0)
REVERT: A  870 HIS cc_start: 0.6813 (OUTLIER) cc_final: 0.6546 (p-80)
REVERT: A  880 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.6756 (mmm-85)
REVERT: A  944 MET cc_start: 0.7319 (tmm) cc_final: 0.6765 (tmm)
REVERT: A  967 THR cc_start: 0.7715 (OUTLIER) cc_final: 0.7316 (m)
REVERT: A 1590 ASN cc_start: 0.8125 (t0) cc_final: 0.7864 (t0)
REVERT: A 1879 PHE cc_start: 0.8617 (m-80) cc_final: 0.8373 (m-10)
REVERT: A 1979 MET cc_start: 0.6411 (mmm) cc_final: 0.5967 (mmm)
  outliers start: 55
  outliers final: 42
  residues processed: 209
  average time/residue: 0.2277
  time to fit residues: 75.9312
Evaluate side-chains
  204 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 157
  time to evaluate  : 1.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   37 PHE
Chi-restraints excluded: chain A residue   38 ILE
Chi-restraints excluded: chain A residue   54 CYS
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  225 CYS
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  493 LEU
Chi-restraints excluded: chain A residue  506 LEU
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  564 LEU
Chi-restraints excluded: chain A residue  577 LEU
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  593 LEU
Chi-restraints excluded: chain A residue  637 VAL
Chi-restraints excluded: chain A residue  708 GLU
Chi-restraints excluded: chain A residue  754 VAL
Chi-restraints excluded: chain A residue  809 VAL
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  870 HIS
Chi-restraints excluded: chain A residue  880 ARG
Chi-restraints excluded: chain A residue  967 THR
Chi-restraints excluded: chain A residue 1004 LEU
Chi-restraints excluded: chain A residue 1075 THR
Chi-restraints excluded: chain A residue 1092 VAL
Chi-restraints excluded: chain A residue 1121 ASP
Chi-restraints excluded: chain A residue 1138 SER
Chi-restraints excluded: chain A residue 1284 SER
Chi-restraints excluded: chain A residue 1323 VAL
Chi-restraints excluded: chain A residue 1455 LEU
Chi-restraints excluded: chain A residue 1458 LEU
Chi-restraints excluded: chain A residue 1569 GLN
Chi-restraints excluded: chain A residue 1586 TRP
Chi-restraints excluded: chain A residue 1643 VAL
Chi-restraints excluded: chain A residue 1693 HIS
Chi-restraints excluded: chain A residue 1701 ILE
Chi-restraints excluded: chain A residue 1841 THR
Chi-restraints excluded: chain A residue 1881 LEU
Chi-restraints excluded: chain A residue 1946 VAL
Chi-restraints excluded: chain A residue 1965 TRP
Chi-restraints excluded: chain A residue 1988 CYS
Chi-restraints excluded: chain A residue 1999 VAL
Chi-restraints excluded: chain A residue 2020 HIS
Chi-restraints excluded: chain A residue 2026 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 119 optimal weight:    5.9990
   chunk 125 optimal weight:    2.9990
   chunk 11 optimal weight:    5.9990
   chunk 157 optimal weight:   20.0000
   chunk 46 optimal weight:    3.9990
   chunk 85 optimal weight:   10.0000
   chunk 69 optimal weight:    8.9990
   chunk 16 optimal weight:   10.0000
   chunk 61 optimal weight:    0.9980
   chunk 115 optimal weight:    0.3980
   chunk 156 optimal weight:    7.9990
   overall best weight:    2.8786

-------------------------------------------------------------------------------
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 = 0.4331 r_free = 0.4331 target = 0.149308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.118640 restraints weight = 37475.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.114364 restraints weight = 38270.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.115772 restraints weight = 38169.374|
|-----------------------------------------------------------------------------|
r_work (final): 0.3840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.2131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  14572  Z= 0.219
  Angle     :  0.736  12.343  19822  Z= 0.354
  Chirality :  0.044   0.301   2258
  Planarity :  0.005   0.057   2544
  Dihedral  :  4.736  27.522   2004
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 13.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 29.30 %
    Favored  : 66.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.10 (0.20), residues: 1826
  helix:  0.43 (0.17), residues: 955
  sheet: -1.95 (0.37), residues: 196
  loop : -1.97 (0.24), residues: 675

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A1965 
 HIS   0.012   0.001   HIS A 996 
 PHE   0.025   0.002   PHE A1584 
 TYR   0.022   0.002   TYR A 560 
 ARG   0.006   0.000   ARG A2056 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03320 (  689)
  hydrogen bonds       : angle       4.82329 ( 2007)
  SS BOND              : bond        0.00286 (    5)
  SS BOND              : angle       0.64828 (   10)
  covalent geometry    : bond        0.00500 (14567)
  covalent geometry    : angle       0.73571 (19812)

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

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

  3652 Ramachandran restraints generated.
    1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3652 Ramachandran restraints generated.
    1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 159
  time to evaluate  : 1.688 
Fit side-chains
   revert: symmetry clash
REVERT: A   16 MET cc_start: 0.9073 (mmm) cc_final: 0.8768 (tpp)
REVERT: A  192 GLN cc_start: 0.7893 (mm-40) cc_final: 0.7646 (pp30)
REVERT: A  577 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8730 (pp)
REVERT: A  588 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7654 (mtm-85)
REVERT: A  708 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6946 (tt0)
REVERT: A  746 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7751 (tt)
REVERT: A  870 HIS cc_start: 0.6872 (OUTLIER) cc_final: 0.6560 (p-80)
REVERT: A  880 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.6901 (mmm-85)
REVERT: A  967 THR cc_start: 0.7754 (OUTLIER) cc_final: 0.7382 (m)
REVERT: A 1590 ASN cc_start: 0.7915 (t0) cc_final: 0.7705 (t0)
REVERT: A 1635 TYR cc_start: 0.7832 (m-80) cc_final: 0.7617 (m-80)
REVERT: A 1879 PHE cc_start: 0.8485 (m-80) cc_final: 0.8270 (m-10)
REVERT: A 1979 MET cc_start: 0.6281 (mmm) cc_final: 0.5981 (mmm)
  outliers start: 59
  outliers final: 45
  residues processed: 205
  average time/residue: 0.2487
  time to fit residues: 81.0410
Evaluate side-chains
  205 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 153
  time to evaluate  : 1.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   37 PHE
Chi-restraints excluded: chain A residue   38 ILE
Chi-restraints excluded: chain A residue   44 HIS
Chi-restraints excluded: chain A residue   54 CYS
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  225 CYS
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  493 LEU
Chi-restraints excluded: chain A residue  577 LEU
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  588 ARG
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain A residue  593 LEU
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  637 VAL
Chi-restraints excluded: chain A residue  672 VAL
Chi-restraints excluded: chain A residue  708 GLU
Chi-restraints excluded: chain A residue  746 LEU
Chi-restraints excluded: chain A residue  754 VAL
Chi-restraints excluded: chain A residue  809 VAL
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  870 HIS
Chi-restraints excluded: chain A residue  880 ARG
Chi-restraints excluded: chain A residue  923 LEU
Chi-restraints excluded: chain A residue  967 THR
Chi-restraints excluded: chain A residue  995 THR
Chi-restraints excluded: chain A residue 1004 LEU
Chi-restraints excluded: chain A residue 1075 THR
Chi-restraints excluded: chain A residue 1092 VAL
Chi-restraints excluded: chain A residue 1121 ASP
Chi-restraints excluded: chain A residue 1138 SER
Chi-restraints excluded: chain A residue 1284 SER
Chi-restraints excluded: chain A residue 1323 VAL
Chi-restraints excluded: chain A residue 1455 LEU
Chi-restraints excluded: chain A residue 1458 LEU
Chi-restraints excluded: chain A residue 1569 GLN
Chi-restraints excluded: chain A residue 1586 TRP
Chi-restraints excluded: chain A residue 1643 VAL
Chi-restraints excluded: chain A residue 1693 HIS
Chi-restraints excluded: chain A residue 1701 ILE
Chi-restraints excluded: chain A residue 1749 LEU
Chi-restraints excluded: chain A residue 1841 THR
Chi-restraints excluded: chain A residue 1868 SER
Chi-restraints excluded: chain A residue 1946 VAL
Chi-restraints excluded: chain A residue 1965 TRP
Chi-restraints excluded: chain A residue 1988 CYS
Chi-restraints excluded: chain A residue 1999 VAL
Chi-restraints excluded: chain A residue 2020 HIS
Chi-restraints excluded: chain A residue 2026 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 54 optimal weight:    0.7980
   chunk 162 optimal weight:    4.9990
   chunk 58 optimal weight:    0.7980
   chunk 158 optimal weight:    3.9990
   chunk 128 optimal weight:    0.8980
   chunk 141 optimal weight:    7.9990
   chunk 159 optimal weight:   40.0000
   chunk 125 optimal weight:    0.3980
   chunk 6 optimal weight:    0.0020
   chunk 91 optimal weight:   10.0000
   chunk 49 optimal weight:    0.7980
   overall best weight:    0.5588

-------------------------------------------------------------------------------
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 = 0.4377 r_free = 0.4377 target = 0.152703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.110449 restraints weight = 37377.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.110545 restraints weight = 27769.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.110979 restraints weight = 19213.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.2122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  14572  Z= 0.114
  Angle     :  0.713  12.187  19822  Z= 0.332
  Chirality :  0.042   0.274   2258
  Planarity :  0.004   0.058   2544
  Dihedral  :  4.544  25.337   2004
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 30.37 %
    Favored  : 66.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.20), residues: 1826
  helix:  0.61 (0.17), residues: 954
  sheet: -1.83 (0.37), residues: 192
  loop : -1.88 (0.24), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP A1965 
 HIS   0.010   0.001   HIS A1887 
 PHE   0.029   0.001   PHE A2037 
 TYR   0.019   0.001   TYR A1591 
 ARG   0.006   0.000   ARG A 938 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03020 (  689)
  hydrogen bonds       : angle       4.63600 ( 2007)
  SS BOND              : bond        0.00229 (    5)
  SS BOND              : angle       0.47321 (   10)
  covalent geometry    : bond        0.00261 (14567)
  covalent geometry    : angle       0.71331 (19812)

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

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

  3652 Ramachandran restraints generated.
    1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3652 Ramachandran restraints generated.
    1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 167
  time to evaluate  : 1.676 
Fit side-chains
REVERT: A   16 MET cc_start: 0.9196 (mmm) cc_final: 0.8777 (tpp)
REVERT: A  192 GLN cc_start: 0.8279 (mm-40) cc_final: 0.7758 (pp30)
REVERT: A  708 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6890 (tt0)
REVERT: A  870 HIS cc_start: 0.6862 (OUTLIER) cc_final: 0.6564 (p-80)
REVERT: A  880 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7094 (mmm-85)
REVERT: A  944 MET cc_start: 0.7785 (tmm) cc_final: 0.7396 (tmm)
REVERT: A  967 THR cc_start: 0.8174 (OUTLIER) cc_final: 0.7760 (m)
REVERT: A 1530 MET cc_start: 0.7118 (ptp) cc_final: 0.6853 (pmm)
REVERT: A 1590 ASN cc_start: 0.8507 (t0) cc_final: 0.8248 (t0)
REVERT: A 1703 MET cc_start: 0.8852 (ppp) cc_final: 0.8571 (ppp)
REVERT: A 1879 PHE cc_start: 0.8973 (m-80) cc_final: 0.8672 (m-10)
REVERT: A 1979 MET cc_start: 0.7216 (mmm) cc_final: 0.6424 (mmm)
  outliers start: 43
  outliers final: 33
  residues processed: 198
  average time/residue: 0.2368
  time to fit residues: 75.0080
Evaluate side-chains
  194 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 157
  time to evaluate  : 1.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   37 PHE
Chi-restraints excluded: chain A residue   38 ILE
Chi-restraints excluded: chain A residue   54 CYS
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  493 LEU
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  593 LEU
Chi-restraints excluded: chain A residue  637 VAL
Chi-restraints excluded: chain A residue  708 GLU
Chi-restraints excluded: chain A residue  754 VAL
Chi-restraints excluded: chain A residue  809 VAL
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  870 HIS
Chi-restraints excluded: chain A residue  880 ARG
Chi-restraints excluded: chain A residue  967 THR
Chi-restraints excluded: chain A residue 1004 LEU
Chi-restraints excluded: chain A residue 1075 THR
Chi-restraints excluded: chain A residue 1092 VAL
Chi-restraints excluded: chain A residue 1121 ASP
Chi-restraints excluded: chain A residue 1284 SER
Chi-restraints excluded: chain A residue 1323 VAL
Chi-restraints excluded: chain A residue 1455 LEU
Chi-restraints excluded: chain A residue 1569 GLN
Chi-restraints excluded: chain A residue 1586 TRP
Chi-restraints excluded: chain A residue 1643 VAL
Chi-restraints excluded: chain A residue 1693 HIS
Chi-restraints excluded: chain A residue 1841 THR
Chi-restraints excluded: chain A residue 1946 VAL
Chi-restraints excluded: chain A residue 1965 TRP
Chi-restraints excluded: chain A residue 1988 CYS
Chi-restraints excluded: chain A residue 1999 VAL
Chi-restraints excluded: chain A residue 2020 HIS
Chi-restraints excluded: chain A residue 2026 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 165 optimal weight:   20.0000
   chunk 172 optimal weight:   20.0000
   chunk 55 optimal weight:    0.9990
   chunk 171 optimal weight:    8.9990
   chunk 94 optimal weight:    4.9990
   chunk 69 optimal weight:   10.0000
   chunk 49 optimal weight:    0.4980
   chunk 136 optimal weight:    1.9990
   chunk 96 optimal weight:    2.9990
   chunk 92 optimal weight:    0.0670
   chunk 67 optimal weight:    0.0170
   overall best weight:    0.7160

-------------------------------------------------------------------------------
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 = 0.4377 r_free = 0.4377 target = 0.152797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.121389 restraints weight = 37831.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.117800 restraints weight = 29811.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.119323 restraints weight = 21744.364|
|-----------------------------------------------------------------------------|
r_work (final): 0.3887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7425
moved from start:          0.2212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  14572  Z= 0.115
  Angle     :  0.707  12.393  19822  Z= 0.327
  Chirality :  0.042   0.287   2258
  Planarity :  0.004   0.058   2544
  Dihedral  :  4.430  25.093   2004
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 30.70 %
    Favored  : 66.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.80 (0.20), residues: 1826
  helix:  0.66 (0.17), residues: 955
  sheet: -1.74 (0.37), residues: 192
  loop : -1.86 (0.24), residues: 679

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.001   TRP A1965 
 HIS   0.011   0.001   HIS A1887 
 PHE   0.028   0.001   PHE A2037 
 TYR   0.019   0.001   TYR A 560 
 ARG   0.004   0.000   ARG A2002 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03013 (  689)
  hydrogen bonds       : angle       4.60275 ( 2007)
  SS BOND              : bond        0.00235 (    5)
  SS BOND              : angle       0.47308 (   10)
  covalent geometry    : bond        0.00265 (14567)
  covalent geometry    : angle       0.70664 (19812)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4345.38 seconds
wall clock time: 76 minutes 42.79 seconds (4602.79 seconds total)