Starting phenix.real_space_refine
on Thu Jul  2 06:19:47 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8gua_34271/07_2026/8gua_34271.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gua_34271/07_2026/8gua_34271.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.77
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gua_34271/07_2026/8gua_34271.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gua_34271/07_2026/8gua_34271.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gua_34271/07_2026/8gua_34271.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gua_34271/07_2026/8gua_34271.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8gua_34271/07_2026/8gua_34271.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8gua_34271/07_2026/8gua_34271.cif"
  }
  resolution = 2.77
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.055
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      62      5.16       5
     C    4481      2.51       5
     N    1204      2.21       5
     O    1267      1.98       5
     F       3      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 7017
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6987
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 855, 6987
          Classifications: {'peptide': 855}
          Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 814}
          Chain breaks: 7
    Chain: "A"
      Number of atoms: 30
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 30
          Unusual residues: {'1LT': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N   ILE A 932 " occ=0.50
      ... (6 atoms not shown)
      pdb=" CD1 ILE A 932 " occ=0.50
    residue:
      pdb=" N   ASP A 933 " occ=0.50
      ... (6 atoms not shown)
      pdb=" OD2 ASP A 933 " occ=0.50
    residue:
      pdb=" N   PHE A 934 " occ=0.50
      ... (9 atoms not shown)
      pdb=" CZ  PHE A 934 " occ=0.50
    residue:
      pdb=" N   GLY A 935 " occ=0.50
      ... (2 atoms not shown)
      pdb=" O   GLY A 935 " occ=0.50
  Time building chain proxies: 1.36, per 1000 atoms: 0.19
  Number of scatterers: 7017
  At special positions: 0
  Unit cell: (79.254, 95.319, 103.887, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      62     16.00
     F       3      9.00
     O    1267      8.00
     N    1204      7.00
     C    4481      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.55
  Conformation dependent library (CDL) restraints added in 372.2 milliseconds
  

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1638

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 7 sheets defined
      51.8% alpha, 12.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 107 through 122
      removed outlier: 3.792A  pdb=" N   ARG A 115 " --> pdb=" O   LYS A 111 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   GLU A 116 " --> pdb=" O   ILE A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 130
      removed outlier: 3.586A  pdb=" N   ASP A 129 " --> pdb=" O   VAL A 125 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   MET A 130 " --> pdb=" O   CYS A 126 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 125 through 130'
    Processing helix  chain 'A' and resid 133 through 141
    Processing helix  chain 'A' and resid 144 through 146
      No H-bonds generated for 'chain 'A' and resid 144 through 146'
    Processing helix  chain 'A' and resid 147 through 155
    Processing helix  chain 'A' and resid 159 through 167
    Processing helix  chain 'A' and resid 178 through 184
    Processing helix  chain 'A' and resid 218 through 229
      removed outlier: 3.971A  pdb=" N   ALA A 222 " --> pdb=" O   GLU A 218 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   GLU A 223 " --> pdb=" O   GLN A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 280
    Processing helix  chain 'A' and resid 290 through 295
    Processing helix  chain 'A' and resid 305 through 309
      removed outlier: 3.642A  pdb=" N   ARG A 309 " --> pdb=" O   SER A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 330
      No H-bonds generated for 'chain 'A' and resid 328 through 330'
    Processing helix  chain 'A' and resid 394 through 396
      No H-bonds generated for 'chain 'A' and resid 394 through 396'
    Processing helix  chain 'A' and resid 488 through 500
      removed outlier: 3.560A  pdb=" N   SER A 499 " --> pdb=" O   HIS A 495 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 525 through 537
      removed outlier: 3.950A  pdb=" N   GLU A 529 " --> pdb=" O   GLU A 525 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LYS A 532 " --> pdb=" O   LYS A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 554
      removed outlier: 3.723A  pdb=" N   HIS A 554 " --> pdb=" O   PHE A 550 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 554 through 559
      removed outlier: 3.668A  pdb=" N   VAL A 559 " --> pdb=" O   ARG A 555 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 561 through 563
      No H-bonds generated for 'chain 'A' and resid 561 through 563'
    Processing helix  chain 'A' and resid 564 through 572
      removed outlier: 3.698A  pdb=" N   LEU A 570 " --> pdb=" O   PRO A 566 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 576 through 589
      removed outlier: 3.515A  pdb=" N   CYS A 585 " --> pdb=" O   ALA A 581 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   LEU A 586 " --> pdb=" O   GLN A 582 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   ASP A 589 " --> pdb=" O   CYS A 585 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 594 through 601
      removed outlier: 4.146A  pdb=" N   GLU A 600 " --> pdb=" O   GLU A 596 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   LEU A 601 " --> pdb=" O   GLN A 597 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 608 through 623
      removed outlier: 3.501A  pdb=" N   ALA A 615 " --> pdb=" O   VAL A 611 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   VAL A 616 " --> pdb=" O   ARG A 612 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 624 through 638
      removed outlier: 4.942A  pdb=" N   ILE A 633 " --> pdb=" O   SER A 629 " (cutoff:3.500A)
      removed outlier: 5.484A  pdb=" N   GLN A 634 " --> pdb=" O   GLN A 630 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   GLN A 637 " --> pdb=" O   ILE A 633 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 647 through 658
      removed outlier: 3.700A  pdb=" N   ARG A 651 " --> pdb=" O   ASN A 647 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 660 through 674
    Processing helix  chain 'A' and resid 680 through 695
      removed outlier: 3.886A  pdb=" N   ALA A 694 " --> pdb=" O   SER A 690 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 697 through 722
      removed outlier: 3.767A  pdb=" N   HIS A 701 " --> pdb=" O   MET A 697 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   GLU A 722 " --> pdb=" O   ILE A 718 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 729 through 740
      removed outlier: 3.729A  pdb=" N   ARG A 740 " --> pdb=" O   VAL A 736 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 741 through 748
      removed outlier: 3.696A  pdb=" N   ALA A 747 " --> pdb=" O   ASP A 743 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 765 through 769
      removed outlier: 3.792A  pdb=" N   CYS A 769 " --> pdb=" O   LEU A 766 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 789 through 793
    Processing helix  chain 'A' and resid 807 through 827
    Processing helix  chain 'A' and resid 857 through 861
    Processing helix  chain 'A' and resid 875 through 884
      removed outlier: 3.503A  pdb=" N   LEU A 881 " --> pdb=" O   LEU A 877 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 889 through 911
      removed outlier: 3.524A  pdb=" N   ALA A 893 " --> pdb=" O   ILE A 889 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   PHE A 897 " --> pdb=" O   ALA A 893 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ARG A 899 " --> pdb=" O   ASP A 895 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   GLY A 903 " --> pdb=" O   ARG A 899 " (cutoff:3.500A)
      removed outlier: 4.420A  pdb=" N   TYR A 904 " --> pdb=" O   SER A 900 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 958 through 965
      removed outlier: 3.939A  pdb=" N   VAL A 963 " --> pdb=" O   ASP A 959 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 974 through 994
      removed outlier: 4.084A  pdb=" N   GLU A 978 " --> pdb=" O   THR A 974 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ARG A 979 " --> pdb=" O   ARG A 975 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   CYS A 984 " --> pdb=" O   PHE A 980 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   TYR A 988 " --> pdb=" O   CYS A 984 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   LEU A 989 " --> pdb=" O   TYR A 985 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   ALA A 990 " --> pdb=" O   LYS A 986 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ILE A 991 " --> pdb=" O   ALA A 987 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 994 through 1001
      removed outlier: 3.801A  pdb=" N   PHE A 998 " --> pdb=" O   HIS A 994 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1004 through 1009
      removed outlier: 4.052A  pdb=" N   GLY A1007 " --> pdb=" O   MET A1004 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   GLY A1009 " --> pdb=" O   LEU A1006 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1010 through 1014
      removed outlier: 3.864A  pdb=" N   GLN A1014 " --> pdb=" O   PRO A1011 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1015 through 1018
    Processing helix  chain 'A' and resid 1019 through 1027
      removed outlier: 4.020A  pdb=" N   ARG A1023 " --> pdb=" O   ILE A1019 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1031 through 1047
      removed outlier: 3.628A  pdb=" N   LEU A1036 " --> pdb=" O   GLU A1032 " (cutoff:3.500A)
      removed outlier: 5.160A  pdb=" N   GLU A1037 " --> pdb=" O   GLN A1033 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   TYR A1038 " --> pdb=" O   GLU A1034 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   PHE A1039 " --> pdb=" O   ALA A1035 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ASP A1045 " --> pdb=" O   LYS A1041 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ALA A1046 " --> pdb=" O   GLN A1042 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 205 through 212
      removed outlier: 3.555A  pdb=" N   ILE A 211 " --> pdb=" O   ILE A 190 " (cutoff:3.500A)
      removed outlier: 8.418A  pdb=" N   LEU A 285 " --> pdb=" O   ILE A 191 " (cutoff:3.500A)
      removed outlier: 5.823A  pdb=" N   VAL A 193 " --> pdb=" O   LEU A 285 " (cutoff:3.500A)
      removed outlier: 7.534A  pdb=" N   LEU A 287 " --> pdb=" O   VAL A 193 " (cutoff:3.500A)
      removed outlier: 7.014A  pdb=" N   TRP A 195 " --> pdb=" O   LEU A 287 " (cutoff:3.500A)
      removed outlier: 8.767A  pdb=" N   ALA A 289 " --> pdb=" O   TRP A 195 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 325 through 326
      removed outlier: 6.407A  pdb=" N   LYS A 325 " --> pdb=" O   LYS A 485 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 382 through 392
      removed outlier: 6.764A  pdb=" N   TRP A 383 " --> pdb=" O   CYS A 340 " (cutoff:3.500A)
      removed outlier: 7.218A  pdb=" N   CYS A 340 " --> pdb=" O   TRP A 383 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   LEU A 334 " --> pdb=" O   TYR A 389 " (cutoff:3.500A)
      removed outlier: 7.147A  pdb=" N   GLU A 474 " --> pdb=" O   LEU A 339 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   ALA A 341 " --> pdb=" O   CYS A 472 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   CYS A 472 " --> pdb=" O   ALA A 341 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 365 through 366
      removed outlier: 3.902A  pdb=" N   GLU A 365 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   LEU A 402 " --> pdb=" O   ASN A 426 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   ASN A 426 " --> pdb=" O   LEU A 402 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   LEU A 404 " --> pdb=" O   TRP A 424 " (cutoff:3.500A)
      removed outlier: 4.589A  pdb=" N   TRP A 424 " --> pdb=" O   LEU A 404 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   ILE A 406 " --> pdb=" O   LEU A 422 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 752 through 753
      removed outlier: 5.727A  pdb=" N   HIS A 759 " --> pdb=" O   SER A 753 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 770 through 771
      removed outlier: 3.514A  pdb=" N   GLY A 846 " --> pdb=" O   LYS A 802 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   VAL A 845 " --> pdb=" O   ILE A 841 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 854 through 856
      removed outlier: 3.528A  pdb=" N   HIS A 855 " --> pdb=" O   VAL A 923 " (cutoff:3.500A)

    279 hydrogen bonds defined for protein.
    801 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: 0.72

  Time building geometry restraints manager: 0.74 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 1160
        1.30 -     1.43: 1820
        1.43 -     1.56: 4092
        1.56 -     1.68: 7
        1.68 -     1.81: 94
  Bond restraints: 7173
  Sorted by residual:
  bond pdb=" C9  1LT A1101 "
       pdb=" S   1LT A1101 "
    ideal  model  delta    sigma   weight residual
    1.738  1.530  0.208 2.00e-02 2.50e+03 1.08e+02
  bond pdb=" C2  1LT A1101 "
       pdb=" S   1LT A1101 "
    ideal  model  delta    sigma   weight residual
    1.734  1.533  0.201 2.00e-02 2.50e+03 1.01e+02
  bond pdb=" N   1LT A1101 "
       pdb=" C1  1LT A1101 "
    ideal  model  delta    sigma   weight residual
    1.368  1.568 -0.200 2.00e-02 2.50e+03 1.00e+02
  bond pdb=" C5  1LT A1101 "
       pdb=" C6  1LT A1101 "
    ideal  model  delta    sigma   weight residual
    1.525  1.350  0.175 2.00e-02 2.50e+03 7.62e+01
  bond pdb=" N   1LT A1101 "
       pdb=" C2  1LT A1101 "
    ideal  model  delta    sigma   weight residual
    1.291  1.415 -0.124 2.00e-02 2.50e+03 3.84e+01
  ... (remaining 7168 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.84: 9656
        3.84 -     7.67: 34
        7.67 -    11.50: 2
       11.50 -    15.34: 2
       15.34 -    19.17: 2
  Bond angle restraints: 9696
  Sorted by residual:
  angle pdb=" N1  1LT A1101 "
        pdb=" C2  1LT A1101 "
        pdb=" S   1LT A1101 "
      ideal   model   delta    sigma   weight residual
     118.47  137.64  -19.17 3.00e+00 1.11e-01 4.09e+01
  angle pdb=" C   TRP A 446 "
        pdb=" N   PRO A 447 "
        pdb=" CA  PRO A 447 "
      ideal   model   delta    sigma   weight residual
     120.03  113.74    6.29 9.90e-01 1.02e+00 4.04e+01
  angle pdb=" C2  1LT A1101 "
        pdb=" S   1LT A1101 "
        pdb=" C9  1LT A1101 "
      ideal   model   delta    sigma   weight residual
      88.90  107.66  -18.76 3.00e+00 1.11e-01 3.91e+01
  angle pdb=" N   1LT A1101 "
        pdb=" C2  1LT A1101 "
        pdb=" N1  1LT A1101 "
      ideal   model   delta    sigma   weight residual
     126.74  114.29   12.45 3.00e+00 1.11e-01 1.72e+01
  angle pdb=" N   PRO A 449 "
        pdb=" CA  PRO A 449 "
        pdb=" C   PRO A 449 "
      ideal   model   delta    sigma   weight residual
     112.47  120.27   -7.80 2.06e+00 2.36e-01 1.43e+01
  ... (remaining 9691 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 3866
       17.85 -    35.69: 406
       35.69 -    53.54: 63
       53.54 -    71.39: 13
       71.39 -    89.24: 7
  Dihedral angle restraints: 4355
    sinusoidal: 1837
      harmonic: 2518
  Sorted by residual:
  dihedral pdb=" C   PHE A 937 "
           pdb=" N   PHE A 937 "
           pdb=" CA  PHE A 937 "
           pdb=" CB  PHE A 937 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.55    8.95     0      2.50e+00 1.60e-01 1.28e+01
  dihedral pdb=" N   PHE A 937 "
           pdb=" C   PHE A 937 "
           pdb=" CA  PHE A 937 "
           pdb=" CB  PHE A 937 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  130.99   -8.19     0      2.50e+00 1.60e-01 1.07e+01
  dihedral pdb=" CA  PRO A 539 "
           pdb=" C   PRO A 539 "
           pdb=" N   LEU A 540 "
           pdb=" CA  LEU A 540 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.70   16.30     0      5.00e+00 4.00e-02 1.06e+01
  ... (remaining 4352 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 966
       0.069 -    0.139: 82
       0.139 -    0.208: 2
       0.208 -    0.278: 2
       0.278 -    0.347: 2
  Chirality restraints: 1054
  Sorted by residual:
  chirality pdb=" CA  PRO A 449 "
            pdb=" N   PRO A 449 "
            pdb=" C   PRO A 449 "
            pdb=" CB  PRO A 449 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.37    0.35 2.00e-01 2.50e+01 3.02e+00
  chirality pdb=" CA  PHE A 937 "
            pdb=" N   PHE A 937 "
            pdb=" C   PHE A 937 "
            pdb=" CB  PHE A 937 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.63e+00
  chirality pdb=" CA  LEU A 938 "
            pdb=" N   LEU A 938 "
            pdb=" C   LEU A 938 "
            pdb=" CB  LEU A 938 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.39e+00
  ... (remaining 1051 not shown)

  Planarity restraints: 1238
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 448 "   -0.069 5.00e-02 4.00e+02   1.03e-01 1.70e+01
        pdb=" N   PRO A 449 "    0.178 5.00e-02 4.00e+02
        pdb=" CA  PRO A 449 "   -0.056 5.00e-02 4.00e+02
        pdb=" CD  PRO A 449 "   -0.054 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 159 "    0.017 2.00e-02 2.50e+03   3.66e-02 1.34e+01
        pdb=" C   PRO A 159 "   -0.063 2.00e-02 2.50e+03
        pdb=" O   PRO A 159 "    0.025 2.00e-02 2.50e+03
        pdb=" N   HIS A 160 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A 858 "   -0.011 2.00e-02 2.50e+03   2.15e-02 4.60e+00
        pdb=" C   MET A 858 "    0.037 2.00e-02 2.50e+03
        pdb=" O   MET A 858 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   GLN A 859 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1235 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1076
        2.76 -     3.29: 6880
        3.29 -     3.83: 11606
        3.83 -     4.36: 14524
        4.36 -     4.90: 23807
  Nonbonded interactions: 57893
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 900 "
            pdb=" O   LEU A 929 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" OH  TYR A 584 "
            pdb=" OD1 ASP A 608 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" O   GLU A 722 "
            pdb=" NE2 GLN A 731 "
     model   vdw
     2.245 3.120
  nonbonded pdb=" NH1 ARG A 808 "
            pdb=" O   SER A1008 "
     model   vdw
     2.248 3.120
  nonbonded pdb=" NE2 GLN A 825 "
            pdb=" O   LEU A 831 "
     model   vdw
     2.251 3.120
  ... (remaining 57888 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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.460
  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:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.040
  Set scattering table:                    0.020
  Process input model:                     6.680
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  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:5.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6137
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      :  0.007   0.208   7173  Z= 0.347
  Angle     :  0.695  19.175   9696  Z= 0.345
  Chirality :  0.044   0.347   1054
  Planarity :  0.005   0.103   1238
  Dihedral  : 14.825  89.236   2717
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  3.81 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.77 %
    Favored  : 99.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.79 (0.29), residues: 839
  helix: -0.84 (0.27), residues: 363
  sheet:  0.24 (0.51), residues: 98
  loop : -0.20 (0.35), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 382 
 TYR   0.024   0.001   TYR A 392 
 PHE   0.012   0.001   PHE A 960 
 TRP   0.005   0.001   TRP A 783 
 HIS   0.003   0.001   HIS A 160 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00686 /  0.35 ( 7173)
  covalent geometry    : angle       0.69461 /  0.35 ( 9696)
  hydrogen bonds       : bond        0.27639 / 18.16 (  279)
  hydrogen bonds       : angle       8.36492 /  5.83 (  801)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 103
  time to evaluate  : 0.162 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 103
  average time/residue: 0.4375
  time to fit residues: 47.6484
Evaluate side-chains
  78 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 643 GLN
** A 796 ASN ** 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 = 0.4546 r_free = 0.4546 target = 0.227965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.202866 restraints weight = 6472.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.4330 rms_B_bonded: 1.17
r_work: 0.4127 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3992 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3992
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3960
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3960 r_free = 0.3960    target_work(ls_wunit_k1) = 0.165         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3957 r_free = 0.3957    target_work(ls_wunit_k1) = 0.165         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (11 function evaluations)
r_final: 0.3957
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6491
moved from start:          0.1505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   7173  Z= 0.172
  Angle     :  0.639   6.312   9696  Z= 0.334
  Chirality :  0.044   0.222   1054
  Planarity :  0.006   0.100   1238
  Dihedral  :  4.824  35.997    929
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.53 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 10.20 %
    Favored  : 88.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.73 (0.29), residues: 839
  helix: -0.53 (0.25), residues: 391
  sheet:  0.44 (0.50), residues: 98
  loop : -0.51 (0.35), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 382 
 TYR   0.020   0.002   TYR A 392 
 PHE   0.014   0.002   PHE A 937 
 TRP   0.007   0.001   TRP A 669 
 HIS   0.004   0.001   HIS A 936 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00396 /  0.17 ( 7173)
  covalent geometry    : angle       0.63911 /  0.33 ( 9696)
  hydrogen bonds       : bond        0.05472 /  3.72 (  279)
  hydrogen bonds       : angle       5.56385 /  3.75 (  801)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
REVERT: A  594 LYS cc_start: 0.7025 (mmtm) cc_final: 0.6367 (mmpt)
REVERT: A  599 MET cc_start: 0.6862 (mtp) cc_final: 0.6461 (mtm)
REVERT: A  682 GLN cc_start: 0.6999 (mp-120) cc_final: 0.6049 (mt0)
REVERT: A  717 ASP cc_start: 0.6956 (OUTLIER) cc_final: 0.6593 (m-30)
REVERT: A  979 ARG cc_start: 0.6654 (OUTLIER) cc_final: 0.5490 (mtt-85)
REVERT: A 1039 PHE cc_start: 0.4765 (t80) cc_final: 0.4455 (t80)
  outliers start: 13
  outliers final: 5
  residues processed: 106
  average time/residue: 0.4250
  time to fit residues: 47.7167
Evaluate side-chains
  92 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 85
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 SER
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  547 GLU
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  717 ASP
Chi-restraints excluded: chain A residue  857 ILE
Chi-restraints excluded: chain A residue  979 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 36 optimal weight:    5.9990
   chunk 64 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9980
   chunk 7 optimal weight:    4.9990
   chunk 80 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 59 optimal weight:    4.9990
   chunk 75 optimal weight:    0.7980
   chunk 72 optimal weight:    3.9990
   overall best weight:    0.8180

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4536 r_free = 0.4536 target = 0.226598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.201157 restraints weight = 6394.427|
|-----------------------------------------------------------------------------|
r_work (start): 0.4306 rms_B_bonded: 1.16
r_work: 0.4102 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3963 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3963
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3939
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3939 r_free = 0.3939    target_work(ls_wunit_k1) = 0.163         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3939 r_free = 0.3939    target_work(ls_wunit_k1) = 0.163         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.3939
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6523
moved from start:          0.1852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   7173  Z= 0.156
  Angle     :  0.611   9.802   9696  Z= 0.315
  Chirality :  0.043   0.219   1054
  Planarity :  0.006   0.096   1238
  Dihedral  :  4.785  36.239    929
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.17 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 14.54 %
    Favored  : 83.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.66 (0.29), residues: 839
  helix: -0.37 (0.25), residues: 391
  sheet:  0.30 (0.49), residues: 98
  loop : -0.54 (0.35), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 382 
 TYR   0.016   0.002   TYR A 392 
 PHE   0.013   0.002   PHE A 666 
 TRP   0.008   0.001   TRP A 386 
 HIS   0.004   0.001   HIS A 665 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00371 /  0.16 ( 7173)
  covalent geometry    : angle       0.61080 /  0.32 ( 9696)
  hydrogen bonds       : bond        0.04706 /  3.25 (  279)
  hydrogen bonds       : angle       5.15082 /  3.46 (  801)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
REVERT: A  278 MET cc_start: 0.4215 (mmp) cc_final: 0.3690 (mtt)
REVERT: A  594 LYS cc_start: 0.7075 (mmtm) cc_final: 0.6423 (mmpt)
REVERT: A  599 MET cc_start: 0.7041 (mtp) cc_final: 0.6601 (mtm)
REVERT: A  682 GLN cc_start: 0.7041 (mp-120) cc_final: 0.6041 (mt0)
REVERT: A  717 ASP cc_start: 0.6966 (OUTLIER) cc_final: 0.6743 (t0)
REVERT: A  979 ARG cc_start: 0.6725 (OUTLIER) cc_final: 0.5755 (mtt-85)
  outliers start: 18
  outliers final: 5
  residues processed: 103
  average time/residue: 0.4283
  time to fit residues: 46.7308
Evaluate side-chains
  94 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 87
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 SER
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  547 GLU
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  717 ASP
Chi-restraints excluded: chain A residue  979 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 36 optimal weight:    7.9990
   chunk 34 optimal weight:    0.7980
   chunk 20 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9980
   chunk 9 optimal weight:    3.9990
   chunk 48 optimal weight:    0.8980
   chunk 31 optimal weight:    0.3980
   chunk 8 optimal weight:    0.8980
   chunk 26 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 637 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4538 r_free = 0.4538 target = 0.226682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.196240 restraints weight = 6491.431|
|-----------------------------------------------------------------------------|
r_work (start): 0.4245 rms_B_bonded: 1.46
r_work: 0.4040 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.4040
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4015
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4015 r_free = 0.4015    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4015 r_free = 0.4015    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.4015
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6448
moved from start:          0.2052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   7173  Z= 0.151
  Angle     :  0.598   7.528   9696  Z= 0.309
  Chirality :  0.043   0.217   1054
  Planarity :  0.006   0.094   1238
  Dihedral  :  4.779  36.537    929
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.41 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 16.33 %
    Favored  : 81.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.57 (0.29), residues: 839
  helix: -0.25 (0.25), residues: 391
  sheet:  0.18 (0.49), residues: 96
  loop : -0.50 (0.35), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 382 
 TYR   0.016   0.002   TYR A 392 
 PHE   0.015   0.002   PHE A 909 
 TRP   0.008   0.001   TRP A 386 
 HIS   0.003   0.001   HIS A 554 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00360 /  0.15 ( 7173)
  covalent geometry    : angle       0.59781 /  0.31 ( 9696)
  hydrogen bonds       : bond        0.04277 /  2.97 (  279)
  hydrogen bonds       : angle       4.95728 /  3.32 (  801)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
REVERT: A  278 MET cc_start: 0.3942 (mmp) cc_final: 0.3362 (mtt)
REVERT: A  374 GLN cc_start: 0.7923 (mp10) cc_final: 0.7640 (mp10)
REVERT: A  594 LYS cc_start: 0.7052 (mmtm) cc_final: 0.6454 (mmpt)
REVERT: A  599 MET cc_start: 0.6881 (mtp) cc_final: 0.6291 (mtm)
REVERT: A  682 GLN cc_start: 0.6941 (mp-120) cc_final: 0.5921 (mt0)
REVERT: A  717 ASP cc_start: 0.6889 (OUTLIER) cc_final: 0.6646 (t0)
REVERT: A  979 ARG cc_start: 0.6620 (OUTLIER) cc_final: 0.5428 (mtt-85)
  outliers start: 20
  outliers final: 3
  residues processed: 102
  average time/residue: 0.4160
  time to fit residues: 44.9226
Evaluate side-chains
  94 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 89
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  717 ASP
Chi-restraints excluded: chain A residue  979 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 35 optimal weight:    9.9990
   chunk 80 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   chunk 60 optimal weight:    0.9990
   chunk 43 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   chunk 47 optimal weight:    0.1980
   chunk 73 optimal weight:    2.9990
   overall best weight:    0.7382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 637 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4537 r_free = 0.4537 target = 0.226567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.199245 restraints weight = 6421.580|
|-----------------------------------------------------------------------------|
r_work (start): 0.4265 rms_B_bonded: 1.33
r_work: 0.4073 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3938 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3938
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3924
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3924 r_free = 0.3924    target_work(ls_wunit_k1) = 0.162         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3924 r_free = 0.3924    target_work(ls_wunit_k1) = 0.162         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.3924
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6508
moved from start:          0.2225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   7173  Z= 0.145
  Angle     :  0.600   6.309   9696  Z= 0.309
  Chirality :  0.043   0.217   1054
  Planarity :  0.006   0.091   1238
  Dihedral  :  4.784  36.514    929
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.53 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 16.84 %
    Favored  : 79.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.51 (0.29), residues: 839
  helix: -0.13 (0.26), residues: 392
  sheet:  0.06 (0.49), residues: 96
  loop : -0.51 (0.35), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 777 
 TYR   0.014   0.002   TYR A 392 
 PHE   0.015   0.002   PHE A 909 
 TRP   0.007   0.001   TRP A 669 
 HIS   0.003   0.001   HIS A 554 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00349 /  0.15 ( 7173)
  covalent geometry    : angle       0.59956 /  0.31 ( 9696)
  hydrogen bonds       : bond        0.04076 /  2.84 (  279)
  hydrogen bonds       : angle       4.81965 /  3.21 (  801)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 89
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
REVERT: A  278 MET cc_start: 0.4469 (mmp) cc_final: 0.3749 (mtt)
REVERT: A  374 GLN cc_start: 0.7928 (mp10) cc_final: 0.7660 (mp10)
REVERT: A  594 LYS cc_start: 0.7143 (mmtm) cc_final: 0.6506 (mmpt)
REVERT: A  599 MET cc_start: 0.7044 (mtp) cc_final: 0.6835 (mtp)
REVERT: A  682 GLN cc_start: 0.7000 (mp-120) cc_final: 0.5965 (mt0)
REVERT: A  717 ASP cc_start: 0.6989 (OUTLIER) cc_final: 0.6756 (t0)
REVERT: A  832 ARG cc_start: 0.5524 (OUTLIER) cc_final: 0.5225 (mmt90)
REVERT: A  979 ARG cc_start: 0.6807 (OUTLIER) cc_final: 0.5612 (mtt-85)
REVERT: A 1004 MET cc_start: 0.6944 (OUTLIER) cc_final: 0.6251 (mmm)
  outliers start: 26
  outliers final: 9
  residues processed: 104
  average time/residue: 0.3388
  time to fit residues: 37.5943
Evaluate side-chains
  99 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 LYS
Chi-restraints excluded: chain A residue  295 SER
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  717 ASP
Chi-restraints excluded: chain A residue  788 ILE
Chi-restraints excluded: chain A residue  832 ARG
Chi-restraints excluded: chain A residue  833 MET
Chi-restraints excluded: chain A residue  979 ARG
Chi-restraints excluded: chain A residue 1004 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 75 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 7 optimal weight:    0.0770
   chunk 47 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0970
   chunk 45 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 25 optimal weight:    0.3980
   chunk 20 optimal weight:    4.9990
   overall best weight:    0.5140

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 450 HIS
A 637 GLN
** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4543 r_free = 0.4543 target = 0.227384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.197642 restraints weight = 6522.000|
|-----------------------------------------------------------------------------|
r_work (start): 0.4272 rms_B_bonded: 1.42
r_work: 0.4073 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.4073
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4060
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4060 r_free = 0.4060    target_work(ls_wunit_k1) = 0.175         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4060 r_free = 0.4060    target_work(ls_wunit_k1) = 0.175         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (11 function evaluations)
r_final: 0.4060
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6409
moved from start:          0.2354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   7173  Z= 0.126
  Angle     :  0.567   7.037   9696  Z= 0.292
  Chirality :  0.042   0.215   1054
  Planarity :  0.005   0.089   1238
  Dihedral  :  4.660  35.663    929
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.29 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 18.88 %
    Favored  : 78.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.33 (0.29), residues: 839
  helix:  0.08 (0.26), residues: 393
  sheet:  0.12 (0.49), residues: 96
  loop : -0.50 (0.35), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 777 
 TYR   0.013   0.001   TYR A 392 
 PHE   0.016   0.002   PHE A 794 
 TRP   0.008   0.001   TRP A 669 
 HIS   0.004   0.001   HIS A 665 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00302 /  0.13 ( 7173)
  covalent geometry    : angle       0.56677 /  0.29 ( 9696)
  hydrogen bonds       : bond        0.03720 /  2.59 (  279)
  hydrogen bonds       : angle       4.66224 /  3.10 (  801)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 90
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
REVERT: A  133 ASP cc_start: 0.6397 (t0) cc_final: 0.5899 (t0)
REVERT: A  138 ASP cc_start: 0.6737 (t70) cc_final: 0.6432 (t70)
REVERT: A  278 MET cc_start: 0.4521 (mmp) cc_final: 0.3774 (mtt)
REVERT: A  374 GLN cc_start: 0.7882 (mp10) cc_final: 0.7626 (mp10)
REVERT: A  594 LYS cc_start: 0.7091 (mmtm) cc_final: 0.6465 (mmpt)
REVERT: A  682 GLN cc_start: 0.6939 (mp-120) cc_final: 0.5943 (mt0)
REVERT: A  697 MET cc_start: 0.7073 (ttp) cc_final: 0.6856 (ttm)
REVERT: A  717 ASP cc_start: 0.6888 (OUTLIER) cc_final: 0.6681 (t0)
REVERT: A  832 ARG cc_start: 0.5601 (OUTLIER) cc_final: 0.5358 (mmt90)
REVERT: A  979 ARG cc_start: 0.6651 (OUTLIER) cc_final: 0.5622 (mtt-85)
REVERT: A  983 MET cc_start: 0.5625 (mtm) cc_final: 0.4425 (ptt)
  outliers start: 24
  outliers final: 4
  residues processed: 106
  average time/residue: 0.3710
  time to fit residues: 42.0552
Evaluate side-chains
  91 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 84
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  717 ASP
Chi-restraints excluded: chain A residue  832 ARG
Chi-restraints excluded: chain A residue  979 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 79 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9980
   chunk 7 optimal weight:    0.2980
   chunk 10 optimal weight:    0.5980
   chunk 32 optimal weight:    3.9990
   chunk 67 optimal weight:    0.8980
   chunk 24 optimal weight:    0.4980
   chunk 59 optimal weight:    0.6980
   chunk 68 optimal weight:    3.9990
   chunk 70 optimal weight:    0.0870
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.4358

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 450 HIS
A 575 ASN
A 637 GLN
** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4552 r_free = 0.4552 target = 0.228639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.199007 restraints weight = 6436.905|
|-----------------------------------------------------------------------------|
r_work (start): 0.4286 rms_B_bonded: 1.42
r_work: 0.4092 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.4092
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4075
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4075 r_free = 0.4075    target_work(ls_wunit_k1) = 0.176         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4075 r_free = 0.4075    target_work(ls_wunit_k1) = 0.176         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.4075
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6385
moved from start:          0.2475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   7173  Z= 0.118
  Angle     :  0.562   7.524   9696  Z= 0.288
  Chirality :  0.042   0.228   1054
  Planarity :  0.005   0.083   1238
  Dihedral  :  4.571  34.805    929
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.41 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 20.54 %
    Favored  : 77.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.18 (0.29), residues: 839
  helix:  0.22 (0.26), residues: 394
  sheet:  0.20 (0.49), residues: 96
  loop : -0.44 (0.35), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 777 
 TYR   0.014   0.001   TYR A 432 
 PHE   0.017   0.002   PHE A 909 
 TRP   0.009   0.001   TRP A 669 
 HIS   0.004   0.001   HIS A 665 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00286 /  0.12 ( 7173)
  covalent geometry    : angle       0.56171 /  0.29 ( 9696)
  hydrogen bonds       : bond        0.03501 /  2.44 (  279)
  hydrogen bonds       : angle       4.50488 /  2.98 (  801)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 93
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
REVERT: A  133 ASP cc_start: 0.6401 (t0) cc_final: 0.5908 (t0)
REVERT: A  138 ASP cc_start: 0.6667 (t70) cc_final: 0.6355 (t70)
REVERT: A  278 MET cc_start: 0.4283 (mmp) cc_final: 0.3613 (mtt)
REVERT: A  682 GLN cc_start: 0.6920 (mp-120) cc_final: 0.5842 (mt0)
REVERT: A  777 ARG cc_start: 0.6948 (mtm110) cc_final: 0.6365 (ptm160)
REVERT: A  821 GLU cc_start: 0.6972 (pp20) cc_final: 0.6720 (tm-30)
REVERT: A  832 ARG cc_start: 0.5630 (OUTLIER) cc_final: 0.5291 (mmt90)
REVERT: A  979 ARG cc_start: 0.6648 (OUTLIER) cc_final: 0.5615 (mtt-85)
REVERT: A  983 MET cc_start: 0.5555 (mtm) cc_final: 0.4393 (ptt)
  outliers start: 17
  outliers final: 5
  residues processed: 104
  average time/residue: 0.3533
  time to fit residues: 39.1445
Evaluate side-chains
  94 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 87
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  832 ARG
Chi-restraints excluded: chain A residue  979 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 26 optimal weight:    6.9990
   chunk 34 optimal weight:    0.7980
   chunk 64 optimal weight:    0.5980
   chunk 75 optimal weight:    0.3980
   chunk 2 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9990
   chunk 65 optimal weight:    0.4980
   chunk 40 optimal weight:    2.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 637 GLN
** A 661 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 = 0.4537 r_free = 0.4537 target = 0.226785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.196949 restraints weight = 6462.249|
|-----------------------------------------------------------------------------|
r_work (start): 0.4268 rms_B_bonded: 1.41
r_work: 0.4076 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.4076
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4060
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4060 r_free = 0.4060    target_work(ls_wunit_k1) = 0.174         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4060 r_free = 0.4060    target_work(ls_wunit_k1) = 0.174         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.4060
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6409
moved from start:          0.2517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   7173  Z= 0.135
  Angle     :  0.577   8.554   9696  Z= 0.298
  Chirality :  0.042   0.230   1054
  Planarity :  0.005   0.080   1238
  Dihedral  :  4.631  34.371    929
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.53 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 21.17 %
    Favored  : 76.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.21 (0.29), residues: 839
  helix:  0.20 (0.26), residues: 394
  sheet:  0.21 (0.50), residues: 96
  loop : -0.49 (0.35), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 777 
 TYR   0.014   0.002   TYR A 432 
 PHE   0.019   0.002   PHE A 960 
 TRP   0.007   0.001   TRP A 669 
 HIS   0.003   0.001   HIS A 554 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00327 /  0.14 ( 7173)
  covalent geometry    : angle       0.57663 /  0.30 ( 9696)
  hydrogen bonds       : bond        0.03649 /  2.55 (  279)
  hydrogen bonds       : angle       4.56120 /  3.01 (  801)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 88
  time to evaluate  : 0.193 
Fit side-chains
REVERT: A  133 ASP cc_start: 0.6431 (t0) cc_final: 0.5942 (t0)
REVERT: A  138 ASP cc_start: 0.6634 (t70) cc_final: 0.6327 (t70)
REVERT: A  278 MET cc_start: 0.4405 (mmp) cc_final: 0.3693 (mtt)
REVERT: A  682 GLN cc_start: 0.6908 (mp-120) cc_final: 0.5865 (mt0)
REVERT: A  832 ARG cc_start: 0.5630 (OUTLIER) cc_final: 0.5350 (mmt90)
REVERT: A  979 ARG cc_start: 0.6643 (OUTLIER) cc_final: 0.5616 (mtt-85)
REVERT: A  983 MET cc_start: 0.5549 (mtm) cc_final: 0.4440 (ptt)
REVERT: A 1033 GLN cc_start: 0.5316 (mp10) cc_final: 0.4799 (mm-40)
REVERT: A 1040 MET cc_start: 0.7233 (OUTLIER) cc_final: 0.5548 (mpt)
  outliers start: 16
  outliers final: 8
  residues processed: 100
  average time/residue: 0.3695
  time to fit residues: 39.4056
Evaluate side-chains
  95 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 SER
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  681 SER
Chi-restraints excluded: chain A residue  788 ILE
Chi-restraints excluded: chain A residue  832 ARG
Chi-restraints excluded: chain A residue  979 ARG
Chi-restraints excluded: chain A residue 1040 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 47 optimal weight:    0.6980
   chunk 53 optimal weight:    0.3980
   chunk 79 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 17 optimal weight:    2.9990
   chunk 52 optimal weight:    0.7980
   chunk 60 optimal weight:    0.4980
   chunk 77 optimal weight:    4.9990
   chunk 84 optimal weight:    0.8980
   chunk 54 optimal weight:    0.8980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 637 GLN
** A 661 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 = 0.4537 r_free = 0.4537 target = 0.226839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.196941 restraints weight = 6514.879|
|-----------------------------------------------------------------------------|
r_work (start): 0.4261 rms_B_bonded: 1.42
r_work: 0.4061 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.4061
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4039
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4039 r_free = 0.4039    target_work(ls_wunit_k1) = 0.173         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4039 r_free = 0.4039    target_work(ls_wunit_k1) = 0.173         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.4039
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6425
moved from start:          0.2557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   7173  Z= 0.139
  Angle     :  0.601   9.579   9696  Z= 0.308
  Chirality :  0.043   0.231   1054
  Planarity :  0.005   0.078   1238
  Dihedral  :  4.678  34.215    929
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.77 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 21.81 %
    Favored  : 76.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.21 (0.29), residues: 839
  helix:  0.25 (0.26), residues: 393
  sheet:  0.23 (0.50), residues: 96
  loop : -0.54 (0.35), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A 777 
 TYR   0.013   0.002   TYR A 432 
 PHE   0.017   0.002   PHE A 909 
 TRP   0.007   0.001   TRP A 669 
 HIS   0.003   0.001   HIS A 554 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00338 /  0.14 ( 7173)
  covalent geometry    : angle       0.60053 /  0.31 ( 9696)
  hydrogen bonds       : bond        0.03651 /  2.54 (  279)
  hydrogen bonds       : angle       4.57729 /  3.02 (  801)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 88
  time to evaluate  : 0.188 
Fit side-chains
REVERT: A  133 ASP cc_start: 0.6455 (t0) cc_final: 0.5971 (t0)
REVERT: A  138 ASP cc_start: 0.6642 (t70) cc_final: 0.6331 (t70)
REVERT: A  278 MET cc_start: 0.4506 (mmp) cc_final: 0.3748 (mtt)
REVERT: A  637 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.7032 (mp-120)
REVERT: A  682 GLN cc_start: 0.7000 (mp-120) cc_final: 0.5922 (mt0)
REVERT: A  832 ARG cc_start: 0.5658 (OUTLIER) cc_final: 0.5403 (mmt90)
REVERT: A  979 ARG cc_start: 0.6662 (OUTLIER) cc_final: 0.5638 (mtt-85)
REVERT: A  983 MET cc_start: 0.5571 (mtm) cc_final: 0.4436 (ptt)
REVERT: A 1033 GLN cc_start: 0.5397 (mp10) cc_final: 0.4883 (mm-40)
REVERT: A 1040 MET cc_start: 0.7317 (OUTLIER) cc_final: 0.5661 (mpt)
  outliers start: 15
  outliers final: 8
  residues processed: 100
  average time/residue: 0.3905
  time to fit residues: 41.5464
Evaluate side-chains
  98 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 SER
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  637 GLN
Chi-restraints excluded: chain A residue  681 SER
Chi-restraints excluded: chain A residue  788 ILE
Chi-restraints excluded: chain A residue  832 ARG
Chi-restraints excluded: chain A residue  979 ARG
Chi-restraints excluded: chain A residue 1040 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9980
   chunk 26 optimal weight:    4.9990
   chunk 81 optimal weight:    6.9990
   chunk 77 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 52 optimal weight:    0.6980
   chunk 54 optimal weight:    0.8980
   chunk 50 optimal weight:    0.8980
   chunk 20 optimal weight:    4.9990
   overall best weight:    0.8980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 637 GLN
** A 661 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 = 0.4526 r_free = 0.4526 target = 0.225582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.195720 restraints weight = 6475.413|
|-----------------------------------------------------------------------------|
r_work (start): 0.4255 rms_B_bonded: 1.40
r_work: 0.4059 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.4059
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4041
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4041 r_free = 0.4041    target_work(ls_wunit_k1) = 0.173         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4041 r_free = 0.4041    target_work(ls_wunit_k1) = 0.173         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (13 function evaluations)
r_final: 0.4041
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6444
moved from start:          0.2593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   7173  Z= 0.162
  Angle     :  0.635   8.997   9696  Z= 0.325
  Chirality :  0.044   0.233   1054
  Planarity :  0.006   0.077   1238
  Dihedral  :  4.805  35.071    929
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 11.56
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.53 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 21.94 %
    Favored  : 76.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.35 (0.29), residues: 839
  helix:  0.14 (0.26), residues: 393
  sheet:  0.09 (0.50), residues: 97
  loop : -0.60 (0.35), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 777 
 TYR   0.015   0.002   TYR A 691 
 PHE   0.019   0.002   PHE A 960 
 TRP   0.007   0.001   TRP A 386 
 HIS   0.003   0.001   HIS A 554 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00394 /  0.16 ( 7173)
  covalent geometry    : angle       0.63516 /  0.32 ( 9696)
  hydrogen bonds       : bond        0.03838 /  2.68 (  279)
  hydrogen bonds       : angle       4.67740 /  3.10 (  801)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 87
  time to evaluate  : 0.197 
Fit side-chains
REVERT: A  133 ASP cc_start: 0.6556 (t0) cc_final: 0.6054 (t0)
REVERT: A  138 ASP cc_start: 0.6660 (t70) cc_final: 0.6342 (t70)
REVERT: A  278 MET cc_start: 0.4610 (mmp) cc_final: 0.3793 (mtt)
REVERT: A  570 LEU cc_start: 0.7602 (mm) cc_final: 0.7400 (mt)
REVERT: A  594 LYS cc_start: 0.7118 (mmtm) cc_final: 0.6484 (mmpt)
REVERT: A  637 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.6970 (mp-120)
REVERT: A  682 GLN cc_start: 0.7012 (mp-120) cc_final: 0.5948 (mt0)
REVERT: A  832 ARG cc_start: 0.5794 (OUTLIER) cc_final: 0.5503 (mmt90)
REVERT: A  979 ARG cc_start: 0.6565 (OUTLIER) cc_final: 0.5495 (mtt-85)
REVERT: A  983 MET cc_start: 0.5606 (mtm) cc_final: 0.4467 (ptt)
REVERT: A 1033 GLN cc_start: 0.5379 (mp10) cc_final: 0.4929 (mm-40)
REVERT: A 1040 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.5610 (mpt)
  outliers start: 14
  outliers final: 8
  residues processed: 96
  average time/residue: 0.3761
  time to fit residues: 38.5211
Evaluate side-chains
  97 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 SER
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  637 GLN
Chi-restraints excluded: chain A residue  681 SER
Chi-restraints excluded: chain A residue  788 ILE
Chi-restraints excluded: chain A residue  832 ARG
Chi-restraints excluded: chain A residue  979 ARG
Chi-restraints excluded: chain A residue 1040 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 71 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0970
   chunk 53 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9980
   chunk 1 optimal weight:    0.4980
   chunk 11 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 65 optimal weight:    0.7980
   chunk 32 optimal weight:    4.9990
   chunk 83 optimal weight:    0.1980
   overall best weight:    0.3978

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 637 GLN
** A 661 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 = 0.4533 r_free = 0.4533 target = 0.226546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.197521 restraints weight = 6450.675|
|-----------------------------------------------------------------------------|
r_work (start): 0.4278 rms_B_bonded: 1.39
r_work: 0.4087 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.4087
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4069
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4069 r_free = 0.4069    target_work(ls_wunit_k1) = 0.175         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4069 r_free = 0.4069    target_work(ls_wunit_k1) = 0.175         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.4069
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6394
moved from start:          0.2617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   7173  Z= 0.125
  Angle     :  0.598   8.852   9696  Z= 0.305
  Chirality :  0.042   0.230   1054
  Planarity :  0.005   0.075   1238
  Dihedral  :  4.707  34.073    929
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.05 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 22.19 %
    Favored  : 76.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.16 (0.29), residues: 839
  helix:  0.32 (0.26), residues: 394
  sheet:  0.28 (0.49), residues: 95
  loop : -0.57 (0.35), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A 777 
 TYR   0.015   0.001   TYR A 432 
 PHE   0.016   0.002   PHE A 909 
 TRP   0.009   0.001   TRP A 669 
 HIS   0.004   0.001   HIS A 665 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00303 /  0.13 ( 7173)
  covalent geometry    : angle       0.59773 /  0.31 ( 9696)
  hydrogen bonds       : bond        0.03490 /  2.43 (  279)
  hydrogen bonds       : angle       4.55431 /  3.01 (  801)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2002.89 seconds
wall clock time: 34 minutes 56.78 seconds (2096.78 seconds total)