Starting phenix.real_space_refine
on Thu Mar  6 02:15:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jlg_36396/03_2025/8jlg_36396.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jlg_36396/03_2025/8jlg_36396.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.87
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jlg_36396/03_2025/8jlg_36396.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jlg_36396/03_2025/8jlg_36396.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jlg_36396/03_2025/8jlg_36396.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jlg_36396/03_2025/8jlg_36396.cif"
  }
  resolution = 2.87
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.038
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      15      5.16       5
     C    2829      2.51       5
     N     738      2.21       5
     O     844      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 4426
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 923
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 923
          Classifications: {'peptide': 111}
          Link IDs: {'PTRANS': 2, 'TRANS': 108}
    Chain: "B"
      Number of atoms: 3437
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 420, 3437
          Classifications: {'peptide': 420}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 411}
    Chain: "E"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 3.40, per 1000 atoms: 0.77
  Number of scatterers: 4426
  At special positions: 0
  Unit cell: (83.83, 82.17, 92.13, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      15     16.00
     O     844      8.00
     N     738      7.00
     C    2829      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
  Links applied
    BETA1-4
      " NAG E   1 " - " NAG E   2 "
    BETA1-6
      " NAG E   1 " - " FUC E   3 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
    NAG-ASN
      " NAG A 601 " - " ASN A 498 "
      " NAG A 602 " - " ASN A 548 "
      " NAG E   1 " - " ASN A 573 "
  Time building additional restraints: 1.18
  Conformation dependent library (CDL) restraints added in 610.9 milliseconds
  

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1000

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 9 sheets defined
      7.7% alpha, 48.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.63
  Creating SS restraints...
    Processing helix  chain 'A' and resid 480 through 484
      removed outlier: 3.758A  pdb=" N   THR A 484 " --> pdb=" O   ALA A 481 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 929 through 933
      removed outlier: 3.692A  pdb=" N   VAL B 933 " --> pdb=" O   ASN B 930 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 954 through 958
      removed outlier: 3.544A  pdb=" N   LEU B 958 " --> pdb=" O   LYS B 955 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1080 through 1091
    Processing helix  chain 'B' and resid 1210 through 1214
      removed outlier: 4.012A  pdb=" N   VAL B1214 " --> pdb=" O   ILE B1211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1265 through 1273
    Processing sheet with id=AA1, first strand: chain 'A' and resid 485 through 493
      removed outlier: 6.189A  pdb=" N   GLY A 509 " --> pdb=" O   GLY A 489 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   ARG A 491 " --> pdb=" O   GLY A 509 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   TYR A 511 " --> pdb=" O   ARG A 491 " (cutoff:3.500A)
      removed outlier: 6.788A  pdb=" N   GLU A 493 " --> pdb=" O   TYR A 511 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   THR A 500 " --> pdb=" O   LEU A 519 " (cutoff:3.500A)
      removed outlier: 7.245A  pdb=" N   LEU A 521 " --> pdb=" O   THR A 500 " (cutoff:3.500A)
      removed outlier: 7.264A  pdb=" N   GLU A 502 " --> pdb=" O   LEU A 521 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   SER A 523 " --> pdb=" O   GLU A 502 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 515 through 527
    current: chain 'A' and resid 550 through 552
    Processing sheet with id=AA2, first strand: chain 'A' and resid 566 through 567
      removed outlier: 5.939A  pdb=" N   PHE A 546 " --> pdb=" O   VAL A 567 " (cutoff:3.500A)
      removed outlier: 8.608A  pdb=" N   PHE A 545 " --> pdb=" O   LYS A 522 " (cutoff:3.500A)
      removed outlier: 6.864A  pdb=" N   VAL A 524 " --> pdb=" O   PHE A 545 " (cutoff:3.500A)
      removed outlier: 8.159A  pdb=" N   ARG A 547 " --> pdb=" O   VAL A 524 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   PHE A 526 " --> pdb=" O   ARG A 547 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   THR A 500 " --> pdb=" O   LEU A 519 " (cutoff:3.500A)
      removed outlier: 7.245A  pdb=" N   LEU A 521 " --> pdb=" O   THR A 500 " (cutoff:3.500A)
      removed outlier: 7.264A  pdb=" N   GLU A 502 " --> pdb=" O   LEU A 521 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   SER A 523 " --> pdb=" O   GLU A 502 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 500 through 512
    current: chain 'A' and resid 555 through 559
    Processing sheet with id=AA3, first strand: chain 'B' and resid 887 through 890
      removed outlier: 3.581A  pdb=" N   ASP B 887 " --> pdb=" O   LYS B 884 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   LEU B 879 " --> pdb=" O   LEU B1074 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   PHE B1072 " --> pdb=" O   ILE B 881 " (cutoff:3.500A)
      removed outlier: 9.655A  pdb=" N   TYR B 883 " --> pdb=" O   LYS B1070 " (cutoff:3.500A)
      removed outlier: 12.393A  pdb=" N   LYS B1070 " --> pdb=" O   TYR B 883 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 887 through 890
      removed outlier: 3.581A  pdb=" N   ASP B 887 " --> pdb=" O   LYS B 884 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   LEU B 879 " --> pdb=" O   LEU B1074 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   PHE B1072 " --> pdb=" O   ILE B 881 " (cutoff:3.500A)
      removed outlier: 9.655A  pdb=" N   TYR B 883 " --> pdb=" O   LYS B1070 " (cutoff:3.500A)
      removed outlier: 12.393A  pdb=" N   LYS B1070 " --> pdb=" O   TYR B 883 " (cutoff:3.500A)
      removed outlier: 5.783A  pdb=" N   ILE B1069 " --> pdb=" O   LYS B 948 " (cutoff:3.500A)
      removed outlier: 6.957A  pdb=" N   LYS B 948 " --> pdb=" O   ILE B1069 " (cutoff:3.500A)
      removed outlier: 5.623A  pdb=" N   TYR B1071 " --> pdb=" O   TRP B 946 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   TRP B 946 " --> pdb=" O   TYR B1071 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   PHE B 941 " --> pdb=" O   ASN B1021 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   ASP B1037 " --> pdb=" O   ILE B1029 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   ILE B1031 " --> pdb=" O   LEU B1035 " (cutoff:3.500A)
      removed outlier: 5.523A  pdb=" N   LEU B1035 " --> pdb=" O   ILE B1031 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 897 through 900
      removed outlier: 7.303A  pdb=" N   LYS B1052 " --> pdb=" O   ILE B 968 " (cutoff:3.500A)
      removed outlier: 5.100A  pdb=" N   ILE B 968 " --> pdb=" O   LYS B1052 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   ILE B 964 " --> pdb=" O   LYS B1056 " (cutoff:3.500A)
      removed outlier: 5.721A  pdb=" N   ASP B1058 " --> pdb=" O   TYR B 962 " (cutoff:3.500A)
      removed outlier: 4.602A  pdb=" N   TYR B 962 " --> pdb=" O   ASP B1058 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   VAL B 976 " --> pdb=" O   ILE B 964 " (cutoff:3.500A)
      removed outlier: 5.233A  pdb=" N   ASN B 966 " --> pdb=" O   TRP B 974 " (cutoff:3.500A)
      removed outlier: 7.187A  pdb=" N   TRP B 974 " --> pdb=" O   ASN B 966 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 1112 through 1115
    Processing sheet with id=AA7, first strand: chain 'B' and resid 1122 through 1125
    Processing sheet with id=AA8, first strand: chain 'B' and resid 1159 through 1164
      removed outlier: 3.986A  pdb=" N   LYS B1159 " --> pdb=" O   VAL B1185 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ASP B1178 " --> pdb=" O   MET B1223 " (cutoff:3.500A)
      removed outlier: 5.636A  pdb=" N   LYS B1226 " --> pdb=" O   LYS B1234 " (cutoff:3.500A)
      removed outlier: 8.074A  pdb=" N   LYS B1234 " --> pdb=" O   LYS B1226 " (cutoff:3.500A)
      removed outlier: 27.061A  pdb=" N   ASN B1233 " --> pdb=" O   LEU B1254 " (cutoff:3.500A)
      removed outlier: 23.354A  pdb=" N   LEU B1254 " --> pdb=" O   ASN B1233 " (cutoff:3.500A)
      removed outlier: 15.632A  pdb=" N   CYS B1235 " --> pdb=" O   PHE B1252 " (cutoff:3.500A)
      removed outlier: 10.927A  pdb=" N   PHE B1252 " --> pdb=" O   CYS B1235 " (cutoff:3.500A)
      removed outlier: 5.333A  pdb=" N   MET B1237 " --> pdb=" O   ILE B1250 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   GLY B1248 " --> pdb=" O   LEU B1239 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 1159 through 1164
      removed outlier: 3.986A  pdb=" N   LYS B1159 " --> pdb=" O   VAL B1185 " (cutoff:3.500A)
      removed outlier: 5.181A  pdb=" N   ILE B1182 " --> pdb=" O   LEU B1193 " (cutoff:3.500A)

    155 hydrogen bonds defined for protein.
    402 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: 1.36

  Time building geometry restraints manager: 1.33 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 764
        1.32 -     1.45: 1415
        1.45 -     1.58: 2317
        1.58 -     1.71: 0
        1.71 -     1.84: 23
  Bond restraints: 4519
  Sorted by residual:
  bond pdb=" C   ILE B1161 "
       pdb=" N   ILE B1162 "
    ideal  model  delta    sigma   weight residual
    1.330  1.277  0.054 1.26e-02 6.30e+03 1.81e+01
  bond pdb=" CA  SER B1281 "
       pdb=" CB  SER B1281 "
    ideal  model  delta    sigma   weight residual
    1.531  1.466  0.064 1.52e-02 4.33e+03 1.79e+01
  bond pdb=" C   TYR B1001 "
       pdb=" O   TYR B1001 "
    ideal  model  delta    sigma   weight residual
    1.236  1.187  0.048 1.20e-02 6.94e+03 1.62e+01
  bond pdb=" C   ILE B1029 "
       pdb=" O   ILE B1029 "
    ideal  model  delta    sigma   weight residual
    1.236  1.199  0.037 1.02e-02 9.61e+03 1.31e+01
  bond pdb=" C   GLY B 981 "
       pdb=" O   GLY B 981 "
    ideal  model  delta    sigma   weight residual
    1.236  1.190  0.045 1.31e-02 5.83e+03 1.21e+01
  ... (remaining 4514 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.46: 5134
        1.46 -     2.91: 849
        2.91 -     4.37: 102
        4.37 -     5.82: 14
        5.82 -     7.28: 7
  Bond angle restraints: 6106
  Sorted by residual:
  angle pdb=" CA  ASP B1256 "
        pdb=" CB  ASP B1256 "
        pdb=" CG  ASP B1256 "
      ideal   model   delta    sigma   weight residual
     112.60  116.45   -3.85 1.00e+00 1.00e+00 1.48e+01
  angle pdb=" C   PRO B1119 "
        pdb=" N   ASN B1120 "
        pdb=" CA  ASN B1120 "
      ideal   model   delta    sigma   weight residual
     122.65  116.95    5.70 1.60e+00 3.91e-01 1.27e+01
  angle pdb=" OD1 ASN B1103 "
        pdb=" CG  ASN B1103 "
        pdb=" ND2 ASN B1103 "
      ideal   model   delta    sigma   weight residual
     122.60  126.09   -3.49 1.00e+00 1.00e+00 1.22e+01
  angle pdb=" N   PRO B1119 "
        pdb=" CA  PRO B1119 "
        pdb=" CB  PRO B1119 "
      ideal   model   delta    sigma   weight residual
     102.17  105.77   -3.60 1.05e+00 9.07e-01 1.17e+01
  angle pdb=" N   ASN B1120 "
        pdb=" CA  ASN B1120 "
        pdb=" CB  ASN B1120 "
      ideal   model   delta    sigma   weight residual
     110.56  115.28   -4.72 1.46e+00 4.69e-01 1.04e+01
  ... (remaining 6101 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.70: 2606
       22.70 -    45.39: 112
       45.39 -    68.08: 21
       68.08 -    90.77: 3
       90.77 -   113.47: 3
  Dihedral angle restraints: 2745
    sinusoidal: 1182
      harmonic: 1563
  Sorted by residual:
  dihedral pdb=" CA  GLU A 532 "
           pdb=" C   GLU A 532 "
           pdb=" N   GLU A 533 "
           pdb=" CA  GLU A 533 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.39  -21.61     0      5.00e+00 4.00e-02 1.87e+01
  dihedral pdb=" CA  PHE A 499 "
           pdb=" C   PHE A 499 "
           pdb=" N   THR A 500 "
           pdb=" CA  THR A 500 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.62   19.38     0      5.00e+00 4.00e-02 1.50e+01
  dihedral pdb=" C1  NAG A 602 "
           pdb=" C5  NAG A 602 "
           pdb=" O5  NAG A 602 "
           pdb=" C4  NAG A 602 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -64.11   49.36 -113.47     1      3.00e+01 1.11e-03 1.49e+01
  ... (remaining 2742 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.151: 637
       0.151 -    0.301: 33
       0.301 -    0.451: 3
       0.451 -    0.602: 0
       0.602 -    0.752: 1
  Chirality restraints: 674
  Sorted by residual:
  chirality pdb=" C1  FUC E   3 "
            pdb=" O6  NAG E   1 "
            pdb=" C2  FUC E   3 "
            pdb=" O5  FUC E   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.28   -0.12 2.00e-02 2.50e+03 3.32e+01
  chirality pdb=" C1  NAG E   2 "
            pdb=" O4  NAG E   1 "
            pdb=" C2  NAG E   2 "
            pdb=" O5  NAG E   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.30   -0.10 2.00e-02 2.50e+03 2.62e+01
  chirality pdb=" C1  NAG A 602 "
            pdb=" ND2 ASN A 548 "
            pdb=" C2  NAG A 602 "
            pdb=" O5  NAG A 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.65   -0.75 2.00e-01 2.50e+01 1.41e+01
  ... (remaining 671 not shown)

  Planarity restraints: 778
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 573 "   -0.037 2.00e-02 2.50e+03   4.07e-02 2.07e+01
        pdb=" CG  ASN A 573 "    0.015 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 573 "    0.005 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 573 "    0.065 2.00e-02 2.50e+03
        pdb=" C1  NAG E   1 "   -0.049 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 999 "    0.036 2.00e-02 2.50e+03   3.11e-02 1.69e+01
        pdb=" CG  PHE B 999 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 999 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 999 "   -0.036 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 999 "   -0.029 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 999 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 999 "    0.055 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 576 "    0.036 2.00e-02 2.50e+03   2.95e-02 1.53e+01
        pdb=" CG  PHE A 576 "   -0.036 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 576 "   -0.042 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 576 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 576 "    0.041 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 576 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 576 "    0.003 2.00e-02 2.50e+03
  ... (remaining 775 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 493
        2.75 -     3.29: 4092
        3.29 -     3.83: 7101
        3.83 -     4.36: 9176
        4.36 -     4.90: 15739
  Nonbonded interactions: 36601
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN B1216 "
            pdb=" ND2 ASN B1242 "
     model   vdw
     2.213 3.120
  nonbonded pdb=" O   TRP B1266 "
            pdb=" NE2 GLN B1270 "
     model   vdw
     2.215 3.120
  nonbonded pdb=" NH2 ARG A 570 "
            pdb=" O7  NAG A 602 "
     model   vdw
     2.262 3.120
  nonbonded pdb=" OH  TYR B 980 "
            pdb=" O   ILE B1148 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" ND2 ASN B 918 "
            pdb=" O   ASP B1062 "
     model   vdw
     2.304 3.120
  ... (remaining 36596 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.840
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     15.400
  Find NCS groups from input model:        0.050
  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:12.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
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      :  0.011   0.090   4519  Z= 0.724
  Angle     :  1.114   7.277   6106  Z= 0.685
  Chirality :  0.085   0.752    674
  Planarity :  0.009   0.103    775
  Dihedral  : 13.811 113.467   1745
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.01 (0.35), residues: 527
  helix:  1.04 (1.04), residues: 23
  sheet: -0.34 (0.33), residues: 233
  loop : -1.07 (0.36), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.009   TRP B1282 
 HIS   0.008   0.004   HIS A 506 
 PHE   0.055   0.012   PHE B 999 
 TYR   0.040   0.010   TYR B1122 
 ARG   0.027   0.003   ARG B1175 

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

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

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.529 
Fit side-chains
REVERT: B 1000 LYS cc_start: 0.8796 (mtpp) cc_final: 0.8354 (mttp)
REVERT: B 1052 LYS cc_start: 0.7817 (mttt) cc_final: 0.7607 (ttmt)
REVERT: B 1118 ASP cc_start: 0.6869 (t70) cc_final: 0.6535 (t70)
REVERT: B 1130 ILE cc_start: 0.7908 (mp) cc_final: 0.7637 (tp)
REVERT: B 1266 TRP cc_start: 0.6567 (t60) cc_final: 0.6314 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 92
  average time/residue: 1.2835
  time to fit residues: 122.7937
Evaluate side-chains
  64 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.547 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 44 optimal weight:    0.0670
   chunk 40 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 13 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9980
   overall best weight:    0.6718

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

Flipped N/Q/H residues before XYZ refinement:
A 504 GLN
B 988 GLN
B1188 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.167003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.129028 restraints weight = 5032.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.3508 rms_B_bonded: 2.44
r_work: 0.3384 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3238 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.1286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4519  Z= 0.201
  Angle     :  0.546  10.092   6106  Z= 0.297
  Chirality :  0.050   0.378    674
  Planarity :  0.003   0.031    775
  Dihedral  :  9.095  89.611    687
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 11.07 %
    Favored  : 86.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.80 (0.35), residues: 527
  helix:  1.50 (1.04), residues: 23
  sheet: -0.16 (0.34), residues: 220
  loop : -0.97 (0.35), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B1266 
 HIS   0.002   0.000   HIS A 506 
 PHE   0.016   0.001   PHE A 497 
 TYR   0.013   0.001   TYR B1149 
 ARG   0.003   0.000   ARG B1179 

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

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

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 1.511 
Fit side-chains
   revert: symmetry clash
REVERT: A  527 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8695 (mt-10)
REVERT: B 1000 LYS cc_start: 0.8549 (mtpp) cc_final: 0.8096 (mttp)
REVERT: B 1052 LYS cc_start: 0.8196 (mttt) cc_final: 0.7691 (ttmt)
REVERT: B 1118 ASP cc_start: 0.6946 (t70) cc_final: 0.6742 (t70)
REVERT: B 1130 ILE cc_start: 0.8469 (mp) cc_final: 0.8109 (tp)
REVERT: B 1189 LYS cc_start: 0.7609 (tttt) cc_final: 0.7298 (mtpp)
REVERT: B 1190 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.6693 (tp30)
REVERT: B 1203 GLU cc_start: 0.8581 (mp0) cc_final: 0.8373 (mp0)
REVERT: B 1266 TRP cc_start: 0.6517 (t60) cc_final: 0.6310 (t60)
  outliers start: 10
  outliers final: 4
  residues processed: 79
  average time/residue: 2.0633
  time to fit residues: 169.4927
Evaluate side-chains
  66 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 61
  time to evaluate  : 0.635 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  482 SER
Chi-restraints excluded: chain A residue  534 CYS
Chi-restraints excluded: chain B residue  926 VAL
Chi-restraints excluded: chain B residue 1081 GLU
Chi-restraints excluded: chain B residue 1190 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 50 optimal weight:    6.9990
   chunk 18 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 7 optimal weight:    0.6980
   chunk 51 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   chunk 28 optimal weight:    8.9990
   chunk 16 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
A 504 GLN
B 988 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.162865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.124735 restraints weight = 5090.141|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 2.45
r_work: 0.3306 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3163 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.1501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   4519  Z= 0.340
  Angle     :  0.595  11.068   6106  Z= 0.317
  Chirality :  0.052   0.385    674
  Planarity :  0.004   0.035    775
  Dihedral  :  8.520  84.208    687
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 13.73 %
    Favored  : 82.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.97 (0.35), residues: 527
  helix:  1.34 (1.04), residues: 23
  sheet: -0.21 (0.33), residues: 232
  loop : -1.18 (0.35), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 974 
 HIS   0.001   0.001   HIS A 494 
 PHE   0.015   0.002   PHE A 497 
 TYR   0.014   0.002   TYR B 962 
 ARG   0.006   0.000   ARG A 570 

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

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

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 65
  time to evaluate  : 0.518 
Fit side-chains
REVERT: A  517 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8478 (pp)
REVERT: A  532 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8020 (tt0)
REVERT: B 1118 ASP cc_start: 0.7028 (t70) cc_final: 0.6812 (t70)
REVERT: B 1130 ILE cc_start: 0.8506 (mp) cc_final: 0.8104 (tp)
REVERT: B 1189 LYS cc_start: 0.7570 (tttt) cc_final: 0.7258 (mtpp)
REVERT: B 1190 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.6855 (tp30)
REVERT: B 1266 TRP cc_start: 0.6474 (t60) cc_final: 0.6254 (t60)
  outliers start: 16
  outliers final: 10
  residues processed: 74
  average time/residue: 1.2734
  time to fit residues: 98.0422
Evaluate side-chains
  74 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 61
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  482 SER
Chi-restraints excluded: chain A residue  484 THR
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  528 ASP
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain A residue  532 GLU
Chi-restraints excluded: chain A residue  534 CYS
Chi-restraints excluded: chain A residue  569 SER
Chi-restraints excluded: chain B residue  926 VAL
Chi-restraints excluded: chain B residue 1018 THR
Chi-restraints excluded: chain B residue 1020 THR
Chi-restraints excluded: chain B residue 1081 GLU
Chi-restraints excluded: chain B residue 1190 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 44 optimal weight:    0.0270
   chunk 48 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 24 optimal weight:    0.6980
   chunk 42 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   chunk 35 optimal weight:    0.3980
   chunk 16 optimal weight:    4.9990
   overall best weight:    0.5638

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

Flipped N/Q/H residues before XYZ refinement:
A 504 GLN
B 988 GLN
B1022 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.165316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.127671 restraints weight = 5040.394|
|-----------------------------------------------------------------------------|
r_work (start): 0.3465 rms_B_bonded: 2.44
r_work: 0.3346 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3206 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.1740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4519  Z= 0.166
  Angle     :  0.522  11.622   6106  Z= 0.278
  Chirality :  0.048   0.326    674
  Planarity :  0.003   0.024    775
  Dihedral  :  7.535  72.887    687
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 17.01 %
    Favored  : 80.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.74 (0.35), residues: 527
  helix:  1.73 (1.08), residues: 23
  sheet: -0.11 (0.34), residues: 230
  loop : -0.98 (0.35), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B1266 
 HIS   0.001   0.000   HIS A 506 
 PHE   0.044   0.002   PHE A 497 
 TYR   0.011   0.001   TYR B1149 
 ARG   0.004   0.000   ARG A 570 

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

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

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 0.478 
Fit side-chains
REVERT: B 1052 LYS cc_start: 0.8052 (mttt) cc_final: 0.7487 (ttmt)
REVERT: B 1118 ASP cc_start: 0.6868 (t70) cc_final: 0.6666 (t70)
REVERT: B 1130 ILE cc_start: 0.8469 (mp) cc_final: 0.8064 (tp)
REVERT: B 1189 LYS cc_start: 0.7465 (tttt) cc_final: 0.7171 (mtpp)
REVERT: B 1190 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6799 (tp30)
REVERT: B 1225 SER cc_start: 0.8517 (t) cc_final: 0.7957 (m)
REVERT: B 1266 TRP cc_start: 0.6433 (t60) cc_final: 0.6173 (t60)
  outliers start: 12
  outliers final: 5
  residues processed: 77
  average time/residue: 1.5198
  time to fit residues: 121.6627
Evaluate side-chains
  68 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 1.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  482 SER
Chi-restraints excluded: chain A residue  484 THR
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain B residue  926 VAL
Chi-restraints excluded: chain B residue 1081 GLU
Chi-restraints excluded: chain B residue 1190 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 12 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 0 optimal weight:    3.9990
   chunk 20 optimal weight:    0.1980
   chunk 11 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 504 GLN
B 988 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.164453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.126731 restraints weight = 5127.896|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 2.47
r_work: 0.3334 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3191 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.1800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4519  Z= 0.211
  Angle     :  0.520   9.969   6106  Z= 0.278
  Chirality :  0.047   0.172    674
  Planarity :  0.003   0.024    775
  Dihedral  :  6.001  35.515    687
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 17.01 %
    Favored  : 79.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.75 (0.35), residues: 527
  helix:  1.79 (1.06), residues: 23
  sheet: -0.05 (0.35), residues: 220
  loop : -1.04 (0.35), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B1266 
 HIS   0.001   0.000   HIS A 494 
 PHE   0.034   0.002   PHE A 497 
 TYR   0.011   0.001   TYR B1149 
 ARG   0.003   0.000   ARG A 570 

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

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

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 69
  time to evaluate  : 0.506 
Fit side-chains
REVERT: A  512 PHE cc_start: 0.7756 (t80) cc_final: 0.7540 (t80)
REVERT: A  517 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8526 (pp)
REVERT: A  532 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8014 (tt0)
REVERT: B 1023 ARG cc_start: 0.7388 (mmm-85) cc_final: 0.7060 (mmt90)
REVERT: B 1130 ILE cc_start: 0.8504 (mp) cc_final: 0.8072 (tp)
REVERT: B 1189 LYS cc_start: 0.7495 (tttt) cc_final: 0.7203 (mtpp)
REVERT: B 1190 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.6821 (tp30)
REVERT: B 1225 SER cc_start: 0.8483 (t) cc_final: 0.7934 (m)
  outliers start: 17
  outliers final: 8
  residues processed: 79
  average time/residue: 1.2268
  time to fit residues: 100.5519
Evaluate side-chains
  75 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  482 SER
Chi-restraints excluded: chain A residue  484 THR
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain A residue  532 GLU
Chi-restraints excluded: chain A residue  534 CYS
Chi-restraints excluded: chain B residue  926 VAL
Chi-restraints excluded: chain B residue 1018 THR
Chi-restraints excluded: chain B residue 1020 THR
Chi-restraints excluded: chain B residue 1081 GLU
Chi-restraints excluded: chain B residue 1190 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 11 optimal weight:    0.0170
   chunk 32 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   chunk 47 optimal weight:    3.9990
   overall best weight:    1.1620

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

Flipped N/Q/H residues before XYZ refinement:
A 504 GLN
B 988 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.163072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.125428 restraints weight = 5025.627|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 2.44
r_work: 0.3313 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3170 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.1914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4519  Z= 0.267
  Angle     :  0.538   9.293   6106  Z= 0.292
  Chirality :  0.048   0.164    674
  Planarity :  0.003   0.028    775
  Dihedral  :  5.628  35.634    687
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 17.21 %
    Favored  : 78.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.35), residues: 527
  helix:  1.58 (1.02), residues: 23
  sheet: -0.14 (0.34), residues: 226
  loop : -1.12 (0.35), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B1266 
 HIS   0.002   0.001   HIS A 494 
 PHE   0.029   0.002   PHE A 497 
 TYR   0.011   0.001   TYR B 962 
 ARG   0.007   0.000   ARG A 570 

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

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

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 63
  time to evaluate  : 0.485 
Fit side-chains
REVERT: A  517 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8708 (pt)
REVERT: A  532 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8019 (tt0)
REVERT: A  570 ARG cc_start: 0.8146 (mtm-85) cc_final: 0.7939 (mtm-85)
REVERT: B 1130 ILE cc_start: 0.8499 (mp) cc_final: 0.8071 (tp)
REVERT: B 1189 LYS cc_start: 0.7494 (tttt) cc_final: 0.7178 (mtpp)
REVERT: B 1190 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6767 (tp30)
REVERT: B 1210 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7775 (mp0)
REVERT: B 1225 SER cc_start: 0.8504 (t) cc_final: 0.7958 (m)
  outliers start: 19
  outliers final: 9
  residues processed: 76
  average time/residue: 1.1397
  time to fit residues: 90.1651
Evaluate side-chains
  74 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 61
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  482 SER
Chi-restraints excluded: chain A residue  484 THR
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain A residue  532 GLU
Chi-restraints excluded: chain A residue  534 CYS
Chi-restraints excluded: chain A residue  569 SER
Chi-restraints excluded: chain B residue  926 VAL
Chi-restraints excluded: chain B residue 1018 THR
Chi-restraints excluded: chain B residue 1020 THR
Chi-restraints excluded: chain B residue 1081 GLU
Chi-restraints excluded: chain B residue 1190 GLU
Chi-restraints excluded: chain B residue 1210 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 19 optimal weight:    0.3980
   chunk 47 optimal weight:    1.9990
   chunk 28 optimal weight:    7.9990
   chunk 52 optimal weight:    0.9980
   chunk 22 optimal weight:    4.9990
   chunk 2 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 504 GLN
B 988 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.163939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.126542 restraints weight = 5038.894|
|-----------------------------------------------------------------------------|
r_work (start): 0.3452 rms_B_bonded: 2.43
r_work: 0.3331 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3188 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.2037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4519  Z= 0.204
  Angle     :  0.505  10.488   6106  Z= 0.274
  Chirality :  0.047   0.166    674
  Planarity :  0.003   0.026    775
  Dihedral  :  5.355  34.573    687
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 18.65 %
    Favored  : 78.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.35), residues: 527
  helix:  1.75 (1.04), residues: 23
  sheet: -0.13 (0.34), residues: 226
  loop : -1.02 (0.35), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B1266 
 HIS   0.001   0.000   HIS A 494 
 PHE   0.025   0.002   PHE A 497 
 TYR   0.011   0.001   TYR B1149 
 ARG   0.005   0.000   ARG A 570 

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

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

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 60
  time to evaluate  : 0.516 
Fit side-chains
REVERT: A  512 PHE cc_start: 0.7685 (t80) cc_final: 0.7467 (t80)
REVERT: A  517 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8518 (pp)
REVERT: A  532 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.7984 (tt0)
REVERT: A  570 ARG cc_start: 0.8187 (mtm-85) cc_final: 0.7940 (mtm-85)
REVERT: B 1056 LYS cc_start: 0.7790 (tttt) cc_final: 0.7533 (pttp)
REVERT: B 1064 ARG cc_start: 0.7288 (mmp-170) cc_final: 0.7000 (mmp80)
REVERT: B 1130 ILE cc_start: 0.8526 (mp) cc_final: 0.8098 (tp)
REVERT: B 1189 LYS cc_start: 0.7458 (tttt) cc_final: 0.7139 (mtpp)
REVERT: B 1190 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6776 (tp30)
REVERT: B 1210 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7742 (mp0)
REVERT: B 1225 SER cc_start: 0.8441 (t) cc_final: 0.7912 (m)
  outliers start: 16
  outliers final: 12
  residues processed: 72
  average time/residue: 1.2148
  time to fit residues: 90.8502
Evaluate side-chains
  76 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 60
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  482 SER
Chi-restraints excluded: chain A residue  484 THR
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain A residue  530 LEU
Chi-restraints excluded: chain A residue  532 GLU
Chi-restraints excluded: chain A residue  534 CYS
Chi-restraints excluded: chain A residue  569 SER
Chi-restraints excluded: chain B residue  926 VAL
Chi-restraints excluded: chain B residue 1018 THR
Chi-restraints excluded: chain B residue 1081 GLU
Chi-restraints excluded: chain B residue 1134 MET
Chi-restraints excluded: chain B residue 1190 GLU
Chi-restraints excluded: chain B residue 1209 LEU
Chi-restraints excluded: chain B residue 1210 GLU
Chi-restraints excluded: chain B residue 1247 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 51 optimal weight:    0.0370
   chunk 14 optimal weight:    0.0670
   chunk 37 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 15 optimal weight:    4.9990
   chunk 13 optimal weight:    0.8980
   chunk 27 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   overall best weight:    0.7398

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

Flipped N/Q/H residues before XYZ refinement:
A 504 GLN
B 988 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.164187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.126862 restraints weight = 5031.877|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 2.42
r_work: 0.3335 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3191 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.2120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4519  Z= 0.194
  Angle     :  0.498  11.082   6106  Z= 0.271
  Chirality :  0.047   0.164    674
  Planarity :  0.003   0.025    775
  Dihedral  :  5.128  33.700    687
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 18.03 %
    Favored  : 78.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.64 (0.35), residues: 527
  helix:  1.74 (1.02), residues: 23
  sheet:  0.25 (0.43), residues: 141
  loop : -0.88 (0.31), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B1266 
 HIS   0.001   0.000   HIS A 494 
 PHE   0.024   0.001   PHE A 497 
 TYR   0.011   0.001   TYR B1149 
 ARG   0.005   0.000   ARG A 570 

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

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

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 61
  time to evaluate  : 0.505 
Fit side-chains
REVERT: A  512 PHE cc_start: 0.7735 (t80) cc_final: 0.7532 (t80)
REVERT: A  517 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8499 (pp)
REVERT: A  532 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8004 (tt0)
REVERT: A  570 ARG cc_start: 0.8196 (mtm-85) cc_final: 0.7822 (mtm-85)
REVERT: B 1064 ARG cc_start: 0.7280 (mmp-170) cc_final: 0.6993 (mmp80)
REVERT: B 1130 ILE cc_start: 0.8500 (mp) cc_final: 0.8062 (tp)
REVERT: B 1189 LYS cc_start: 0.7429 (tttt) cc_final: 0.7169 (mtpp)
REVERT: B 1190 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6773 (tp30)
REVERT: B 1225 SER cc_start: 0.8417 (t) cc_final: 0.7889 (m)
  outliers start: 17
  outliers final: 11
  residues processed: 72
  average time/residue: 1.3390
  time to fit residues: 99.8594
Evaluate side-chains
  68 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 54
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  482 SER
Chi-restraints excluded: chain A residue  484 THR
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain A residue  532 GLU
Chi-restraints excluded: chain A residue  534 CYS
Chi-restraints excluded: chain A residue  569 SER
Chi-restraints excluded: chain B residue  926 VAL
Chi-restraints excluded: chain B residue 1018 THR
Chi-restraints excluded: chain B residue 1020 THR
Chi-restraints excluded: chain B residue 1081 GLU
Chi-restraints excluded: chain B residue 1190 GLU
Chi-restraints excluded: chain B residue 1209 LEU
Chi-restraints excluded: chain B residue 1247 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 47 optimal weight:    3.9990
   chunk 21 optimal weight:    0.0970
   chunk 29 optimal weight:    2.9990
   chunk 26 optimal weight:    0.5980
   chunk 31 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 504 GLN
B 988 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.163167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.125668 restraints weight = 5059.659|
|-----------------------------------------------------------------------------|
r_work (start): 0.3439 rms_B_bonded: 2.44
r_work: 0.3317 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3174 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.2132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4519  Z= 0.249
  Angle     :  0.520  10.602   6106  Z= 0.282
  Chirality :  0.048   0.162    674
  Planarity :  0.003   0.025    775
  Dihedral  :  5.195  33.460    687
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 18.24 %
    Favored  : 78.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.72 (0.35), residues: 527
  helix:  1.70 (1.02), residues: 23
  sheet: -0.23 (0.34), residues: 221
  loop : -0.81 (0.35), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B1266 
 HIS   0.002   0.001   HIS A 494 
 PHE   0.024   0.002   PHE A 497 
 TYR   0.011   0.001   TYR B1149 
 ARG   0.005   0.000   ARG A 570 

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

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

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 56
  time to evaluate  : 0.526 
Fit side-chains
REVERT: A  517 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8700 (pt)
REVERT: A  532 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8035 (tt0)
REVERT: B 1130 ILE cc_start: 0.8521 (mp) cc_final: 0.8062 (tp)
REVERT: B 1189 LYS cc_start: 0.7485 (tttt) cc_final: 0.7191 (mtpp)
REVERT: B 1190 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6786 (tp30)
REVERT: B 1225 SER cc_start: 0.8423 (t) cc_final: 0.7893 (m)
  outliers start: 16
  outliers final: 10
  residues processed: 67
  average time/residue: 1.3264
  time to fit residues: 92.2148
Evaluate side-chains
  71 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 58
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  482 SER
Chi-restraints excluded: chain A residue  484 THR
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain A residue  532 GLU
Chi-restraints excluded: chain A residue  534 CYS
Chi-restraints excluded: chain A residue  569 SER
Chi-restraints excluded: chain B residue  926 VAL
Chi-restraints excluded: chain B residue 1018 THR
Chi-restraints excluded: chain B residue 1020 THR
Chi-restraints excluded: chain B residue 1081 GLU
Chi-restraints excluded: chain B residue 1190 GLU
Chi-restraints excluded: chain B residue 1209 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 24 optimal weight:    0.3980
   chunk 49 optimal weight:    0.8980
   chunk 42 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 27 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 504 GLN
B 988 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.163996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.126693 restraints weight = 4995.030|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 2.41
r_work: 0.3332 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3190 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.2215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4519  Z= 0.207
  Angle     :  0.502  11.649   6106  Z= 0.272
  Chirality :  0.047   0.167    674
  Planarity :  0.003   0.025    775
  Dihedral  :  5.099  32.685    687
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 18.65 %
    Favored  : 78.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.65 (0.35), residues: 527
  helix:  1.83 (1.03), residues: 23
  sheet: -0.19 (0.35), residues: 211
  loop : -0.75 (0.34), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B1266 
 HIS   0.003   0.001   HIS B1253 
 PHE   0.022   0.002   PHE A 497 
 TYR   0.011   0.001   TYR B1149 
 ARG   0.005   0.000   ARG A 570 

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

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

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1054 Ramachandran restraints generated.
    527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 56
  time to evaluate  : 0.544 
Fit side-chains
REVERT: A  517 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8710 (pt)
REVERT: A  532 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8020 (tt0)
REVERT: B  988 GLN cc_start: 0.7814 (mt0) cc_final: 0.7280 (mt0)
REVERT: B 1064 ARG cc_start: 0.7286 (mmp-170) cc_final: 0.6990 (mmp80)
REVERT: B 1130 ILE cc_start: 0.8521 (mp) cc_final: 0.8066 (tp)
REVERT: B 1189 LYS cc_start: 0.7488 (tttt) cc_final: 0.7199 (mtpp)
REVERT: B 1190 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6769 (tp30)
REVERT: B 1225 SER cc_start: 0.8419 (t) cc_final: 0.7909 (m)
  outliers start: 14
  outliers final: 11
  residues processed: 65
  average time/residue: 1.2473
  time to fit residues: 84.2828
Evaluate side-chains
  69 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 55
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  482 SER
Chi-restraints excluded: chain A residue  484 THR
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain A residue  530 LEU
Chi-restraints excluded: chain A residue  532 GLU
Chi-restraints excluded: chain A residue  534 CYS
Chi-restraints excluded: chain A residue  569 SER
Chi-restraints excluded: chain B residue  926 VAL
Chi-restraints excluded: chain B residue 1018 THR
Chi-restraints excluded: chain B residue 1020 THR
Chi-restraints excluded: chain B residue 1081 GLU
Chi-restraints excluded: chain B residue 1190 GLU
Chi-restraints excluded: chain B residue 1209 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0470
   chunk 24 optimal weight:    0.0980
   chunk 19 optimal weight:    0.5980
   chunk 13 optimal weight:    0.8980
   chunk 14 optimal weight:    0.8980
   chunk 49 optimal weight:    3.9990
   chunk 40 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 17 optimal weight:    4.9990
   chunk 44 optimal weight:    0.6980
   overall best weight:    0.4478

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

Flipped N/Q/H residues before XYZ refinement:
A 504 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.166179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.128837 restraints weight = 5066.516|
|-----------------------------------------------------------------------------|
r_work (start): 0.3463 rms_B_bonded: 2.44
r_work: 0.3343 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3201 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.2302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   4519  Z= 0.147
  Angle     :  0.473  12.271   6106  Z= 0.257
  Chirality :  0.046   0.174    674
  Planarity :  0.002   0.025    775
  Dihedral  :  4.855  31.232    687
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 18.85 %
    Favored  : 78.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.48 (0.36), residues: 527
  helix:  2.03 (1.04), residues: 23
  sheet: -0.11 (0.36), residues: 206
  loop : -0.62 (0.34), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B1266 
 HIS   0.001   0.000   HIS B1253 
 PHE   0.021   0.001   PHE A 497 
 TYR   0.010   0.001   TYR B1149 
 ARG   0.005   0.000   ARG A 570 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4334.07 seconds
wall clock time: 77 minutes 2.89 seconds (4622.89 seconds total)