Starting phenix.real_space_refine
on Thu Jul 24 21:45:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9u3u_63827/07_2025/9u3u_63827.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9u3u_63827/07_2025/9u3u_63827.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9u3u_63827/07_2025/9u3u_63827.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9u3u_63827/07_2025/9u3u_63827.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9u3u_63827/07_2025/9u3u_63827.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9u3u_63827/07_2025/9u3u_63827.cif"
  }
  resolution = 3.5
  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=   0.002 sd=   0.027
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      49      5.16       5
     C    4347      2.51       5
     N    1101      2.21       5
     O    1205      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6702
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 6702
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 848, 6702
          Classifications: {'peptide': 848}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 825}
          Chain breaks: 9
          Unresolved non-hydrogen bonds: 71
          Unresolved non-hydrogen angles: 77
          Unresolved non-hydrogen dihedrals: 65
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 14
  Time building chain proxies: 4.47, per 1000 atoms: 0.67
  Number of scatterers: 6702
  At special positions: 0
  Unit cell: (64.64, 88.88, 150.49, 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      49     16.00
     O    1205      8.00
     N    1101      7.00
     C    4347      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 217 " - pdb=" SG  CYS A 268 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.75
  Conformation dependent library (CDL) restraints added in 955.2 milliseconds
  

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1598

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 6 sheets defined
      67.9% alpha, 15.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.99
  Creating SS restraints...
    Processing helix  chain 'A' and resid 98 through 138
      Proline residue:  A 110  - end of helix
    Processing helix  chain 'A' and resid 142 through 165
      removed outlier: 3.667A  pdb=" N   ALA A 147 " --> pdb=" O   ILE A 143 " (cutoff:3.500A)
      Proline residue:  A 148  - end of helix
      removed outlier: 4.066A  pdb=" N   PHE A 164 " --> pdb=" O   PHE A 160 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   THR A 165 " --> pdb=" O   LEU A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 171
      removed outlier: 3.727A  pdb=" N   ALA A 169 " --> pdb=" O   THR A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 195
      removed outlier: 3.972A  pdb=" N   LEU A 195 " --> pdb=" O   GLN A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 219 through 237
      removed outlier: 3.745A  pdb=" N   SER A 223 " --> pdb=" O   SER A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 263
    Processing helix  chain 'A' and resid 279 through 336
      removed outlier: 3.989A  pdb=" N   LEU A 329 " --> pdb=" O   VAL A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 341 through 345
    Processing helix  chain 'A' and resid 402 through 408
    Processing helix  chain 'A' and resid 411 through 434
    Processing helix  chain 'A' and resid 457 through 481
    Processing helix  chain 'A' and resid 511 through 523
      removed outlier: 3.548A  pdb=" N   ASN A 515 " --> pdb=" O   SER A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 532 through 537
    Processing helix  chain 'A' and resid 549 through 555
    Processing helix  chain 'A' and resid 756 through 765
    Processing helix  chain 'A' and resid 765 through 774
    Processing helix  chain 'A' and resid 782 through 810
      removed outlier: 3.531A  pdb=" N   THR A 804 " --> pdb=" O   THR A 800 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   TYR A 809 " --> pdb=" O   CYS A 805 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 817 through 844
    Processing helix  chain 'A' and resid 849 through 860
    Processing helix  chain 'A' and resid 861 through 882
      Proline residue:  A 876  - end of helix
      removed outlier: 3.568A  pdb=" N   ALA A 879 " --> pdb=" O   LEU A 875 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   VAL A 880 " --> pdb=" O   PRO A 876 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   TYR A 881 " --> pdb=" O   ALA A 877 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 895 through 909
      removed outlier: 3.777A  pdb=" N   ILE A 904 " --> pdb=" O   SER A 900 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   TYR A 909 " --> pdb=" O   ALA A 905 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 916 through 928
    Processing helix  chain 'A' and resid 929 through 937
    Processing helix  chain 'A' and resid 978 through 1034
      removed outlier: 3.642A  pdb=" N   VAL A 983 " --> pdb=" O   GLY A 979 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1037 through 1047
      removed outlier: 3.564A  pdb=" N   ALA A1041 " --> pdb=" O   PRO A1037 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   GLU A1042 " --> pdb=" O   TYR A1038 " (cutoff:3.500A)
      removed outlier: 4.487A  pdb=" N   GLN A1043 " --> pdb=" O   HIS A1039 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1066 through 1071
    Processing helix  chain 'A' and resid 1081 through 1098
      removed outlier: 3.835A  pdb=" N   LEU A1095 " --> pdb=" O   ASP A1091 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   LEU A1096 " --> pdb=" O   PHE A1092 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   SER A1097 " --> pdb=" O   ASP A1093 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1099 through 1102
      removed outlier: 3.723A  pdb=" N   SER A1102 " --> pdb=" O   PRO A1099 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1099 through 1102'
    Processing helix  chain 'A' and resid 1132 through 1144
    Processing helix  chain 'A' and resid 1144 through 1153
    Processing helix  chain 'A' and resid 1188 through 1200
    Processing helix  chain 'A' and resid 1209 through 1220
      removed outlier: 4.181A  pdb=" N   VAL A1215 " --> pdb=" O   GLU A1211 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   SER A1217 " --> pdb=" O   TYR A1213 " (cutoff:3.500A)
      removed outlier: 5.397A  pdb=" N   LYS A1218 " --> pdb=" O   ARG A1214 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   MET A1219 " --> pdb=" O   VAL A1215 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   GLY A1220 " --> pdb=" O   LEU A1216 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 387 through 388
      removed outlier: 3.839A  pdb=" N   CYS A 497 " --> pdb=" O   GLN A 388 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 400 through 401
      removed outlier: 3.891A  pdb=" N   VAL A 401 " --> pdb=" O   ASN A 485 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   ASN A 485 " --> pdb=" O   VAL A 401 " (cutoff:3.500A)
      removed outlier: 8.015A  pdb=" N   TYR A 446 " --> pdb=" O   ILE A 438 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   ILE A 438 " --> pdb=" O   TYR A 446 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 400 through 401
      removed outlier: 3.891A  pdb=" N   VAL A 401 " --> pdb=" O   ASN A 485 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   ASN A 485 " --> pdb=" O   VAL A 401 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   MET A 486 " --> pdb=" O   LYS A 528 " (cutoff:3.500A)
      removed outlier: 7.855A  pdb=" N   HIS A 530 " --> pdb=" O   MET A 486 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   VAL A 488 " --> pdb=" O   HIS A 530 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1104 through 1110
      removed outlier: 5.232A  pdb=" N   LYS A1106 " --> pdb=" O   ALA A1117 " (cutoff:3.500A)
      removed outlier: 6.195A  pdb=" N   ALA A1117 " --> pdb=" O   LYS A1106 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   LYS A1108 " --> pdb=" O   MET A1115 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   SER A1051 " --> pdb=" O   VAL A1176 " (cutoff:3.500A)
      removed outlier: 7.674A  pdb=" N   VAL A1176 " --> pdb=" O   SER A1051 " (cutoff:3.500A)
      removed outlier: 6.153A  pdb=" N   ASN A1053 " --> pdb=" O   ALA A1174 " (cutoff:3.500A)
      removed outlier: 7.428A  pdb=" N   ALA A1174 " --> pdb=" O   ASN A1053 " (cutoff:3.500A)
      removed outlier: 5.798A  pdb=" N   ASP A1055 " --> pdb=" O   LEU A1172 " (cutoff:3.500A)
      removed outlier: 5.754A  pdb=" N   LEU A1172 " --> pdb=" O   ASP A1055 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ASN A1168 " --> pdb=" O   VAL A1059 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1104 through 1110
      removed outlier: 5.232A  pdb=" N   LYS A1106 " --> pdb=" O   ALA A1117 " (cutoff:3.500A)
      removed outlier: 6.195A  pdb=" N   ALA A1117 " --> pdb=" O   LYS A1106 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   LYS A1108 " --> pdb=" O   MET A1115 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   SER A1051 " --> pdb=" O   VAL A1176 " (cutoff:3.500A)
      removed outlier: 7.674A  pdb=" N   VAL A1176 " --> pdb=" O   SER A1051 " (cutoff:3.500A)
      removed outlier: 6.153A  pdb=" N   ASN A1053 " --> pdb=" O   ALA A1174 " (cutoff:3.500A)
      removed outlier: 7.428A  pdb=" N   ALA A1174 " --> pdb=" O   ASN A1053 " (cutoff:3.500A)
      removed outlier: 5.798A  pdb=" N   ASP A1055 " --> pdb=" O   LEU A1172 " (cutoff:3.500A)
      removed outlier: 5.754A  pdb=" N   LEU A1172 " --> pdb=" O   ASP A1055 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ASN A1168 " --> pdb=" O   VAL A1059 " (cutoff:3.500A)
      removed outlier: 8.829A  pdb=" N   GLN A1207 " --> pdb=" O   LEU A1163 " (cutoff:3.500A)
      removed outlier: 7.695A  pdb=" N   VAL A1165 " --> pdb=" O   GLN A1207 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1224 through 1231
      removed outlier: 5.224A  pdb=" N   TYR A1225 " --> pdb=" O   LEU A1241 " (cutoff:3.500A)
      removed outlier: 5.621A  pdb=" N   LEU A1241 " --> pdb=" O   TYR A1225 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   GLY A1227 " --> pdb=" O   THR A1239 " (cutoff:3.500A)

    477 hydrogen bonds defined for protein.
    1401 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: 3.20

  Time building geometry restraints manager: 2.07 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2120
        1.34 -     1.46: 1697
        1.46 -     1.58: 2963
        1.58 -     1.70: 0
        1.70 -     1.82: 72
  Bond restraints: 6852
  Sorted by residual:
  bond pdb=" CB  ASP A1015 "
       pdb=" CG  ASP A1015 "
    ideal  model  delta    sigma   weight residual
    1.516  1.546 -0.030 2.50e-02 1.60e+03 1.46e+00
  bond pdb=" CA  ILE A 400 "
       pdb=" CB  ILE A 400 "
    ideal  model  delta    sigma   weight residual
    1.530  1.541 -0.011 1.05e-02 9.07e+03 1.01e+00
  bond pdb=" CB  ASP A 443 "
       pdb=" CG  ASP A 443 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 2.50e-02 1.60e+03 9.41e-01
  bond pdb=" CB  ASN A1168 "
       pdb=" CG  ASN A1168 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 2.50e-02 1.60e+03 9.36e-01
  bond pdb=" CD2 TYR A1213 "
       pdb=" CE2 TYR A1213 "
    ideal  model  delta    sigma   weight residual
    1.382  1.354  0.028 3.00e-02 1.11e+03 8.63e-01
  ... (remaining 6847 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.94: 9173
        1.94 -     3.88: 88
        3.88 -     5.83: 18
        5.83 -     7.77: 3
        7.77 -     9.71: 1
  Bond angle restraints: 9283
  Sorted by residual:
  angle pdb=" CB  MET A 545 "
        pdb=" CG  MET A 545 "
        pdb=" SD  MET A 545 "
      ideal   model   delta    sigma   weight residual
     112.70  122.41   -9.71 3.00e+00 1.11e-01 1.05e+01
  angle pdb=" CA  MET A 849 "
        pdb=" CB  MET A 849 "
        pdb=" CG  MET A 849 "
      ideal   model   delta    sigma   weight residual
     114.10  118.99   -4.89 2.00e+00 2.50e-01 5.97e+00
  angle pdb=" N   MET A 138 "
        pdb=" CA  MET A 138 "
        pdb=" C   MET A 138 "
      ideal   model   delta    sigma   weight residual
     110.44  107.58    2.86 1.20e+00 6.94e-01 5.70e+00
  angle pdb=" CA  VAL A 237 "
        pdb=" CB  VAL A 237 "
        pdb=" CG2 VAL A 237 "
      ideal   model   delta    sigma   weight residual
     110.40  114.27   -3.87 1.70e+00 3.46e-01 5.19e+00
  angle pdb=" CA  TYR A1240 "
        pdb=" CB  TYR A1240 "
        pdb=" CG  TYR A1240 "
      ideal   model   delta    sigma   weight residual
     113.90  117.95   -4.05 1.80e+00 3.09e-01 5.05e+00
  ... (remaining 9278 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.73: 3378
       17.73 -    35.47: 479
       35.47 -    53.20: 131
       53.20 -    70.93: 24
       70.93 -    88.66: 5
  Dihedral angle restraints: 4017
    sinusoidal: 1545
      harmonic: 2472
  Sorted by residual:
  dihedral pdb=" CA  TYR A 235 "
           pdb=" C   TYR A 235 "
           pdb=" N   THR A 236 "
           pdb=" CA  THR A 236 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.10  -15.90     0      5.00e+00 4.00e-02 1.01e+01
  dihedral pdb=" CG  ARG A 264 "
           pdb=" CD  ARG A 264 "
           pdb=" NE  ARG A 264 "
           pdb=" CZ  ARG A 264 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -136.58  -43.42     2      1.50e+01 4.44e-03 1.01e+01
  dihedral pdb=" CA  THR A 236 "
           pdb=" C   THR A 236 "
           pdb=" N   VAL A 237 "
           pdb=" CA  VAL A 237 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.43  -15.57     0      5.00e+00 4.00e-02 9.70e+00
  ... (remaining 4014 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 980
       0.063 -    0.127: 83
       0.127 -    0.190: 0
       0.190 -    0.253: 0
       0.253 -    0.316: 1
  Chirality restraints: 1064
  Sorted by residual:
  chirality pdb=" CB  VAL A 237 "
            pdb=" CA  VAL A 237 "
            pdb=" CG1 VAL A 237 "
            pdb=" CG2 VAL A 237 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.31   -0.32 2.00e-01 2.50e+01 2.50e+00
  chirality pdb=" CA  ILE A1064 "
            pdb=" N   ILE A1064 "
            pdb=" C   ILE A1064 "
            pdb=" CB  ILE A1064 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.94e-01
  chirality pdb=" CA  ILE A1104 "
            pdb=" N   ILE A1104 "
            pdb=" C   ILE A1104 "
            pdb=" CB  ILE A1104 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.90e-01
  ... (remaining 1061 not shown)

  Planarity restraints: 1159
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 240 "   -0.033 5.00e-02 4.00e+02   4.98e-02 3.97e+00
        pdb=" N   PRO A 241 "    0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO A 241 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 241 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 930 "    0.026 5.00e-02 4.00e+02   3.94e-02 2.48e+00
        pdb=" N   PRO A 931 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 931 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 931 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 761 "    0.081 9.50e-02 1.11e+02   3.66e-02 1.02e+00
        pdb=" NE  ARG A 761 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 761 "    0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 761 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 761 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1156 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 445
        2.74 -     3.28: 7054
        3.28 -     3.82: 11335
        3.82 -     4.36: 13066
        4.36 -     4.90: 21973
  Nonbonded interactions: 53873
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 799 "
            pdb=" OG1 THR A 803 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" O   LYS A 434 "
            pdb=" NH2 ARG A 455 "
     model   vdw
     2.233 3.120
  nonbonded pdb=" OE1 GLU A 770 "
            pdb=" OG1 THR A 784 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" ND2 ASN A 748 "
            pdb=" OG  SER A 751 "
     model   vdw
     2.295 3.120
  nonbonded pdb=" O   GLU A 331 "
            pdb=" ND1 HIS A 335 "
     model   vdw
     2.317 3.120
  ... (remaining 53868 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.150
  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:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.730
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6550
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      :  0.002   0.030   6853  Z= 0.104
  Angle     :  0.506   9.711   9285  Z= 0.258
  Chirality :  0.036   0.316   1064
  Planarity :  0.003   0.050   1159
  Dihedral  : 17.922  88.662   2416
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  : 32.23 %
    Favored  : 67.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  0.92 (0.30), residues: 828
  helix:  1.19 (0.22), residues: 528
  sheet: -0.28 (0.71), residues: 59
  loop : -0.28 (0.43), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP A1030 
 HIS   0.003   0.001   HIS A 292 
 PHE   0.016   0.001   PHE A 785 
 TYR   0.009   0.001   TYR A1213 
 ARG   0.008   0.000   ARG A 761 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.25365 (  461)
  hydrogen bonds       : angle       7.91371 ( 1401)
  SS BOND              : bond        0.00008 (    1)
  SS BOND              : angle       0.18232 (    2)
  covalent geometry    : bond        0.00226 ( 6852)
  covalent geometry    : angle       0.50590 ( 9283)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 154
  time to evaluate  : 0.733 
Fit side-chains
   revert: symmetry clash
REVERT: A  798 PHE cc_start: 0.7553 (t80) cc_final: 0.7235 (t80)
REVERT: A 1156 MET cc_start: 0.7530 (tpp) cc_final: 0.7180 (mmm)
REVERT: A 1197 MET cc_start: 0.7191 (OUTLIER) cc_final: 0.6939 (mtt)
  outliers start: 3
  outliers final: 0
  residues processed: 155
  average time/residue: 0.2695
  time to fit residues: 53.5932
Evaluate side-chains
  140 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 139
  time to evaluate  : 1.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1197 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    0.7980
   chunk 63 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0770
   chunk 21 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9980
   chunk 34 optimal weight:    0.5980
   chunk 65 optimal weight:    0.8980
   chunk 25 optimal weight:    0.5980
   chunk 40 optimal weight:    3.9990
   chunk 49 optimal weight:    0.7980
   chunk 76 optimal weight:    2.9990
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
A 292 HIS
** A 911 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 = 0.4183 r_free = 0.4183 target = 0.166700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.141898 restraints weight = 9794.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.146353 restraints weight = 5458.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.149402 restraints weight = 3715.580|
|-----------------------------------------------------------------------------|
r_work (final): 0.3972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6579
moved from start:          0.1793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6853  Z= 0.148
  Angle     :  0.559   7.985   9285  Z= 0.301
  Chirality :  0.040   0.231   1064
  Planarity :  0.004   0.048   1159
  Dihedral  :  4.080  22.471    914
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 28.08 %
    Favored  : 67.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  1.68 (0.29), residues: 828
  helix:  1.97 (0.21), residues: 538
  sheet:  0.02 (0.63), residues: 71
  loop : -0.62 (0.44), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 862 
 HIS   0.004   0.001   HIS A 137 
 PHE   0.013   0.001   PHE A 897 
 TYR   0.023   0.002   TYR A1240 
 ARG   0.003   0.000   ARG A 920 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05456 (  461)
  hydrogen bonds       : angle       5.03366 ( 1401)
  SS BOND              : bond        0.00023 (    1)
  SS BOND              : angle       0.11059 (    2)
  covalent geometry    : bond        0.00302 ( 6852)
  covalent geometry    : angle       0.55867 ( 9283)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 169
  time to evaluate  : 0.720 
Fit side-chains
REVERT: A  143 ILE cc_start: 0.5963 (OUTLIER) cc_final: 0.5706 (pt)
REVERT: A  162 PHE cc_start: 0.6170 (t80) cc_final: 0.5949 (t80)
REVERT: A  301 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7894 (mmt)
REVERT: A  340 ARG cc_start: 0.5958 (OUTLIER) cc_final: 0.5648 (mtm-85)
REVERT: A  406 MET cc_start: 0.4266 (OUTLIER) cc_final: 0.3989 (mtm)
REVERT: A  787 SER cc_start: 0.8243 (t) cc_final: 0.7776 (m)
REVERT: A 1025 ARG cc_start: 0.6415 (tpp80) cc_final: 0.6077 (tpp80)
REVERT: A 1114 TYR cc_start: 0.8205 (t80) cc_final: 0.6355 (t80)
REVERT: A 1162 LYS cc_start: 0.7079 (pttt) cc_final: 0.6753 (pttt)
REVERT: A 1219 MET cc_start: 0.2332 (ttm) cc_final: 0.2109 (ttm)
  outliers start: 35
  outliers final: 15
  residues processed: 188
  average time/residue: 0.2081
  time to fit residues: 51.2925
Evaluate side-chains
  178 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 159
  time to evaluate  : 0.795 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 ILE
Chi-restraints excluded: chain A residue  145 MET
Chi-restraints excluded: chain A residue  227 CYS
Chi-restraints excluded: chain A residue  301 MET
Chi-restraints excluded: chain A residue  319 HIS
Chi-restraints excluded: chain A residue  340 ARG
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  446 TYR
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  828 LEU
Chi-restraints excluded: chain A residue  849 MET
Chi-restraints excluded: chain A residue  866 HIS
Chi-restraints excluded: chain A residue  872 LEU
Chi-restraints excluded: chain A residue  875 LEU
Chi-restraints excluded: chain A residue  991 LEU
Chi-restraints excluded: chain A residue 1202 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 36 optimal weight:    0.0870
   chunk 25 optimal weight:    0.6980
   chunk 55 optimal weight:    0.0060
   chunk 0 optimal weight:    8.9990
   chunk 76 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 50 optimal weight:    0.4980
   chunk 20 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 73 optimal weight:    4.9990
   overall best weight:    0.4374

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

Flipped N/Q/H residues before XYZ refinement:
A 292 HIS
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1009 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.167018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.141775 restraints weight = 9969.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.146267 restraints weight = 5571.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.149407 restraints weight = 3802.430|
|-----------------------------------------------------------------------------|
r_work (final): 0.3960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6573
moved from start:          0.2294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6853  Z= 0.130
  Angle     :  0.527   6.973   9285  Z= 0.281
  Chirality :  0.038   0.177   1064
  Planarity :  0.004   0.050   1159
  Dihedral  :  3.967  15.988    911
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 28.77 %
    Favored  : 67.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  1.90 (0.29), residues: 828
  helix:  2.16 (0.21), residues: 531
  sheet:  0.02 (0.62), residues: 76
  loop : -0.48 (0.45), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 510 
 HIS   0.002   0.001   HIS A1169 
 PHE   0.026   0.001   PHE A 987 
 TYR   0.017   0.001   TYR A1240 
 ARG   0.005   0.000   ARG A 761 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04709 (  461)
  hydrogen bonds       : angle       4.64184 ( 1401)
  SS BOND              : bond        0.00002 (    1)
  SS BOND              : angle       0.10254 (    2)
  covalent geometry    : bond        0.00266 ( 6852)
  covalent geometry    : angle       0.52694 ( 9283)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 164
  time to evaluate  : 0.750 
Fit side-chains
REVERT: A  162 PHE cc_start: 0.6229 (t80) cc_final: 0.5980 (t80)
REVERT: A  240 LEU cc_start: 0.6930 (OUTLIER) cc_final: 0.6488 (mp)
REVERT: A  301 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7802 (mmt)
REVERT: A  396 LEU cc_start: 0.7915 (mt) cc_final: 0.7653 (tt)
REVERT: A  406 MET cc_start: 0.4182 (OUTLIER) cc_final: 0.3913 (mtm)
REVERT: A  512 ASN cc_start: 0.6265 (OUTLIER) cc_final: 0.6004 (t0)
REVERT: A  787 SER cc_start: 0.8256 (t) cc_final: 0.7772 (m)
REVERT: A  798 PHE cc_start: 0.7780 (t80) cc_final: 0.7367 (t80)
REVERT: A 1025 ARG cc_start: 0.6331 (tpp80) cc_final: 0.6125 (tpp80)
REVERT: A 1094 GLU cc_start: 0.6330 (tm-30) cc_final: 0.5920 (tm-30)
REVERT: A 1106 LYS cc_start: 0.6920 (OUTLIER) cc_final: 0.6133 (ptmt)
REVERT: A 1114 TYR cc_start: 0.8221 (t80) cc_final: 0.7142 (t80)
REVERT: A 1162 LYS cc_start: 0.7028 (pttt) cc_final: 0.6523 (pttt)
  outliers start: 24
  outliers final: 13
  residues processed: 177
  average time/residue: 0.2005
  time to fit residues: 46.4175
Evaluate side-chains
  174 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 156
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 MET
Chi-restraints excluded: chain A residue  227 CYS
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  301 MET
Chi-restraints excluded: chain A residue  334 ILE
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  446 TYR
Chi-restraints excluded: chain A residue  512 ASN
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  531 ILE
Chi-restraints excluded: chain A residue  784 THR
Chi-restraints excluded: chain A residue  849 MET
Chi-restraints excluded: chain A residue  866 HIS
Chi-restraints excluded: chain A residue  991 LEU
Chi-restraints excluded: chain A residue 1032 LEU
Chi-restraints excluded: chain A residue 1106 LYS
Chi-restraints excluded: chain A residue 1202 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0870
   chunk 6 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 50 optimal weight:    0.1980
   chunk 9 optimal weight:    4.9990
   chunk 35 optimal weight:    0.6980
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.7760

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

Flipped N/Q/H residues before XYZ refinement:
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.166014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.140396 restraints weight = 9950.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.145006 restraints weight = 5622.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.148146 restraints weight = 3846.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.3953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6622
moved from start:          0.2613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6853  Z= 0.154
  Angle     :  0.534   6.922   9285  Z= 0.283
  Chirality :  0.039   0.167   1064
  Planarity :  0.004   0.050   1159
  Dihedral  :  4.025  15.484    911
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 27.94 %
    Favored  : 67.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  1.88 (0.30), residues: 828
  helix:  2.12 (0.22), residues: 537
  sheet: -0.07 (0.61), residues: 76
  loop : -0.47 (0.45), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 510 
 HIS   0.003   0.001   HIS A 288 
 PHE   0.019   0.001   PHE A1223 
 TYR   0.027   0.002   TYR A1240 
 ARG   0.006   0.001   ARG A 761 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04500 (  461)
  hydrogen bonds       : angle       4.55102 ( 1401)
  SS BOND              : bond        0.00015 (    1)
  SS BOND              : angle       0.09378 (    2)
  covalent geometry    : bond        0.00339 ( 6852)
  covalent geometry    : angle       0.53443 ( 9283)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 165
  time to evaluate  : 0.744 
Fit side-chains
   revert: symmetry clash
REVERT: A  143 ILE cc_start: 0.6032 (OUTLIER) cc_final: 0.5782 (pt)
REVERT: A  301 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7842 (mmm)
REVERT: A  393 VAL cc_start: 0.7512 (OUTLIER) cc_final: 0.7310 (t)
REVERT: A  396 LEU cc_start: 0.7974 (mt) cc_final: 0.7656 (tt)
REVERT: A  406 MET cc_start: 0.4219 (OUTLIER) cc_final: 0.3930 (mtm)
REVERT: A  512 ASN cc_start: 0.6212 (OUTLIER) cc_final: 0.5904 (t0)
REVERT: A  787 SER cc_start: 0.8282 (t) cc_final: 0.7818 (m)
REVERT: A 1015 ASP cc_start: 0.6712 (p0) cc_final: 0.6406 (p0)
REVERT: A 1025 ARG cc_start: 0.6488 (tpp80) cc_final: 0.6279 (tpp80)
REVERT: A 1094 GLU cc_start: 0.6369 (tm-30) cc_final: 0.5979 (tm-30)
REVERT: A 1106 LYS cc_start: 0.6989 (OUTLIER) cc_final: 0.6438 (ptmm)
REVERT: A 1162 LYS cc_start: 0.7006 (OUTLIER) cc_final: 0.6459 (pttt)
  outliers start: 36
  outliers final: 21
  residues processed: 187
  average time/residue: 0.2029
  time to fit residues: 49.9395
Evaluate side-chains
  180 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 152
  time to evaluate  : 0.756 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 ILE
Chi-restraints excluded: chain A residue  145 MET
Chi-restraints excluded: chain A residue  227 CYS
Chi-restraints excluded: chain A residue  301 MET
Chi-restraints excluded: chain A residue  319 HIS
Chi-restraints excluded: chain A residue  388 GLN
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  446 TYR
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  510 TRP
Chi-restraints excluded: chain A residue  512 ASN
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  531 ILE
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  784 THR
Chi-restraints excluded: chain A residue  849 MET
Chi-restraints excluded: chain A residue  866 HIS
Chi-restraints excluded: chain A residue  875 LEU
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  991 LEU
Chi-restraints excluded: chain A residue 1032 LEU
Chi-restraints excluded: chain A residue 1106 LYS
Chi-restraints excluded: chain A residue 1162 LYS
Chi-restraints excluded: chain A residue 1202 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 9 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 47 optimal weight:    9.9990
   chunk 24 optimal weight:    0.2980
   chunk 37 optimal weight:    2.9990
   chunk 59 optimal weight:    4.9990
   chunk 41 optimal weight:    7.9990
   chunk 23 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 39 optimal weight:    5.9990
   chunk 57 optimal weight:    0.6980
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1009 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.164496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.139654 restraints weight = 9798.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.143895 restraints weight = 5677.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.146836 restraints weight = 3959.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.3924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6659
moved from start:          0.2921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6853  Z= 0.197
  Angle     :  0.587   8.501   9285  Z= 0.308
  Chirality :  0.041   0.194   1064
  Planarity :  0.004   0.051   1159
  Dihedral  :  4.215  15.518    911
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 28.91 %
    Favored  : 65.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  1.64 (0.29), residues: 828
  helix:  1.94 (0.21), residues: 538
  sheet: -0.45 (0.60), residues: 78
  loop : -0.46 (0.46), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 510 
 HIS   0.004   0.001   HIS A 288 
 PHE   0.024   0.002   PHE A 798 
 TYR   0.015   0.002   TYR A 909 
 ARG   0.007   0.001   ARG A 761 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04711 (  461)
  hydrogen bonds       : angle       4.65183 ( 1401)
  SS BOND              : bond        0.00035 (    1)
  SS BOND              : angle       0.10258 (    2)
  covalent geometry    : bond        0.00431 ( 6852)
  covalent geometry    : angle       0.58694 ( 9283)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 159
  time to evaluate  : 0.766 
Fit side-chains
REVERT: A  143 ILE cc_start: 0.6247 (OUTLIER) cc_final: 0.6012 (pt)
REVERT: A  240 LEU cc_start: 0.7543 (mm) cc_final: 0.7305 (mt)
REVERT: A  340 ARG cc_start: 0.5975 (OUTLIER) cc_final: 0.5707 (mtm-85)
REVERT: A  406 MET cc_start: 0.4176 (OUTLIER) cc_final: 0.3893 (mtm)
REVERT: A  465 MET cc_start: 0.6965 (OUTLIER) cc_final: 0.5470 (tpt)
REVERT: A  512 ASN cc_start: 0.6176 (OUTLIER) cc_final: 0.5926 (t0)
REVERT: A 1094 GLU cc_start: 0.6357 (tm-30) cc_final: 0.6042 (tm-30)
REVERT: A 1106 LYS cc_start: 0.7014 (OUTLIER) cc_final: 0.6343 (ptmt)
REVERT: A 1162 LYS cc_start: 0.7009 (OUTLIER) cc_final: 0.6452 (pttt)
REVERT: A 1213 TYR cc_start: 0.4410 (m-80) cc_final: 0.4079 (m-10)
REVERT: A 1219 MET cc_start: 0.2232 (ttm) cc_final: 0.1999 (ttm)
  outliers start: 38
  outliers final: 20
  residues processed: 180
  average time/residue: 0.2222
  time to fit residues: 52.6171
Evaluate side-chains
  182 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 155
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 ILE
Chi-restraints excluded: chain A residue  145 MET
Chi-restraints excluded: chain A residue  176 SER
Chi-restraints excluded: chain A residue  227 CYS
Chi-restraints excluded: chain A residue  319 HIS
Chi-restraints excluded: chain A residue  340 ARG
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  446 TYR
Chi-restraints excluded: chain A residue  465 MET
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  500 LEU
Chi-restraints excluded: chain A residue  510 TRP
Chi-restraints excluded: chain A residue  512 ASN
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  531 ILE
Chi-restraints excluded: chain A residue  784 THR
Chi-restraints excluded: chain A residue  849 MET
Chi-restraints excluded: chain A residue  866 HIS
Chi-restraints excluded: chain A residue  875 LEU
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  991 LEU
Chi-restraints excluded: chain A residue 1032 LEU
Chi-restraints excluded: chain A residue 1106 LYS
Chi-restraints excluded: chain A residue 1162 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 7 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9990
   chunk 9 optimal weight:    4.9990
   chunk 33 optimal weight:    0.6980
   chunk 42 optimal weight:    0.7980
   chunk 35 optimal weight:    0.5980
   chunk 49 optimal weight:    9.9990
   chunk 2 optimal weight:    3.9990
   chunk 60 optimal weight:    0.6980
   chunk 40 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1009 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.165130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.140219 restraints weight = 9796.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.144729 restraints weight = 5475.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.147795 restraints weight = 3713.661|
|-----------------------------------------------------------------------------|
r_work (final): 0.3946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6633
moved from start:          0.3089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6853  Z= 0.152
  Angle     :  0.579  10.800   9285  Z= 0.295
  Chirality :  0.039   0.163   1064
  Planarity :  0.004   0.051   1159
  Dihedral  :  4.147  15.303    911
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 30.98 %
    Favored  : 65.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  1.71 (0.30), residues: 828
  helix:  2.05 (0.22), residues: 532
  sheet: -0.15 (0.63), residues: 73
  loop : -0.62 (0.44), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 510 
 HIS   0.003   0.001   HIS A1009 
 PHE   0.017   0.001   PHE A 798 
 TYR   0.012   0.001   TYR A1114 
 ARG   0.007   0.000   ARG A 761 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04395 (  461)
  hydrogen bonds       : angle       4.53152 ( 1401)
  SS BOND              : bond        0.00015 (    1)
  SS BOND              : angle       0.11910 (    2)
  covalent geometry    : bond        0.00333 ( 6852)
  covalent geometry    : angle       0.57931 ( 9283)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 155
  time to evaluate  : 0.688 
Fit side-chains
REVERT: A  143 ILE cc_start: 0.6243 (OUTLIER) cc_final: 0.6017 (pt)
REVERT: A  152 PHE cc_start: 0.5700 (t80) cc_final: 0.5375 (t80)
REVERT: A  240 LEU cc_start: 0.7600 (mm) cc_final: 0.7358 (mt)
REVERT: A  406 MET cc_start: 0.4029 (OUTLIER) cc_final: 0.3737 (mtm)
REVERT: A  448 VAL cc_start: 0.7862 (t) cc_final: 0.7657 (p)
REVERT: A  512 ASN cc_start: 0.6083 (OUTLIER) cc_final: 0.5730 (t0)
REVERT: A 1094 GLU cc_start: 0.6424 (tm-30) cc_final: 0.6045 (tm-30)
REVERT: A 1106 LYS cc_start: 0.6945 (OUTLIER) cc_final: 0.6428 (ptmm)
REVERT: A 1162 LYS cc_start: 0.6975 (OUTLIER) cc_final: 0.6416 (pttt)
REVERT: A 1213 TYR cc_start: 0.4401 (m-80) cc_final: 0.4144 (m-10)
  outliers start: 29
  outliers final: 21
  residues processed: 172
  average time/residue: 0.2092
  time to fit residues: 47.4930
Evaluate side-chains
  174 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 148
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 ILE
Chi-restraints excluded: chain A residue  145 MET
Chi-restraints excluded: chain A residue  176 SER
Chi-restraints excluded: chain A residue  227 CYS
Chi-restraints excluded: chain A residue  319 HIS
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  446 TYR
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  510 TRP
Chi-restraints excluded: chain A residue  512 ASN
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  531 ILE
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  784 THR
Chi-restraints excluded: chain A residue  849 MET
Chi-restraints excluded: chain A residue  866 HIS
Chi-restraints excluded: chain A residue  875 LEU
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  991 LEU
Chi-restraints excluded: chain A residue 1032 LEU
Chi-restraints excluded: chain A residue 1106 LYS
Chi-restraints excluded: chain A residue 1162 LYS
Chi-restraints excluded: chain A residue 1202 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 11 optimal weight:    0.6980
   chunk 63 optimal weight:    2.9990
   chunk 75 optimal weight:    0.1980
   chunk 6 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 71 optimal weight:    0.7980
   chunk 55 optimal weight:    0.6980
   chunk 52 optimal weight:    0.5980
   chunk 81 optimal weight:    0.5980
   chunk 78 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1009 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.165902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.140900 restraints weight = 9771.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.145359 restraints weight = 5480.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.148207 restraints weight = 3744.742|
|-----------------------------------------------------------------------------|
r_work (final): 0.3949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6625
moved from start:          0.3249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6853  Z= 0.133
  Angle     :  0.572  11.212   9285  Z= 0.289
  Chirality :  0.039   0.177   1064
  Planarity :  0.004   0.051   1159
  Dihedral  :  4.066  15.392    911
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 31.26 %
    Favored  : 64.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  1.80 (0.30), residues: 828
  helix:  2.13 (0.22), residues: 532
  sheet: -0.24 (0.61), residues: 78
  loop : -0.58 (0.45), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A1030 
 HIS   0.003   0.001   HIS A 292 
 PHE   0.015   0.001   PHE A 798 
 TYR   0.014   0.001   TYR A 881 
 ARG   0.008   0.001   ARG A 761 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04186 (  461)
  hydrogen bonds       : angle       4.42984 ( 1401)
  SS BOND              : bond        0.00015 (    1)
  SS BOND              : angle       0.11449 (    2)
  covalent geometry    : bond        0.00288 ( 6852)
  covalent geometry    : angle       0.57248 ( 9283)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 156
  time to evaluate  : 0.776 
Fit side-chains
REVERT: A  137 HIS cc_start: 0.6775 (m90) cc_final: 0.6505 (m170)
REVERT: A  152 PHE cc_start: 0.5716 (t80) cc_final: 0.5418 (t80)
REVERT: A  240 LEU cc_start: 0.7617 (mm) cc_final: 0.7382 (mt)
REVERT: A  305 ARG cc_start: 0.7251 (mtt90) cc_final: 0.6980 (mmt-90)
REVERT: A  406 MET cc_start: 0.3945 (OUTLIER) cc_final: 0.3663 (mtm)
REVERT: A  433 THR cc_start: 0.5780 (m) cc_final: 0.4023 (t)
REVERT: A  512 ASN cc_start: 0.6085 (OUTLIER) cc_final: 0.5616 (t0)
REVERT: A 1094 GLU cc_start: 0.6415 (tm-30) cc_final: 0.5980 (tm-30)
REVERT: A 1106 LYS cc_start: 0.6972 (OUTLIER) cc_final: 0.6566 (ttpt)
REVERT: A 1162 LYS cc_start: 0.6978 (OUTLIER) cc_final: 0.6403 (pttt)
  outliers start: 31
  outliers final: 23
  residues processed: 175
  average time/residue: 0.2004
  time to fit residues: 46.0116
Evaluate side-chains
  177 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 150
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 MET
Chi-restraints excluded: chain A residue  176 SER
Chi-restraints excluded: chain A residue  227 CYS
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  319 HIS
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  446 TYR
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  500 LEU
Chi-restraints excluded: chain A residue  510 TRP
Chi-restraints excluded: chain A residue  512 ASN
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  531 ILE
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  784 THR
Chi-restraints excluded: chain A residue  849 MET
Chi-restraints excluded: chain A residue  866 HIS
Chi-restraints excluded: chain A residue  875 LEU
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  991 LEU
Chi-restraints excluded: chain A residue 1032 LEU
Chi-restraints excluded: chain A residue 1106 LYS
Chi-restraints excluded: chain A residue 1162 LYS
Chi-restraints excluded: chain A residue 1202 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 26 optimal weight:    0.3980
   chunk 81 optimal weight:    1.9990
   chunk 41 optimal weight:    7.9990
   chunk 43 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9980
   chunk 70 optimal weight:    0.8980
   chunk 58 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 56 optimal weight:    2.9990
   chunk 23 optimal weight:    0.5980
   chunk 48 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1009 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.165624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.140591 restraints weight = 9750.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.145112 restraints weight = 5441.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.148147 restraints weight = 3694.798|
|-----------------------------------------------------------------------------|
r_work (final): 0.3948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6632
moved from start:          0.3343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6853  Z= 0.152
  Angle     :  0.601  12.940   9285  Z= 0.301
  Chirality :  0.039   0.159   1064
  Planarity :  0.003   0.050   1159
  Dihedral  :  4.130  15.540    911
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 10.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 30.84 %
    Favored  : 64.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  1.76 (0.30), residues: 828
  helix:  2.04 (0.22), residues: 538
  sheet: -0.34 (0.60), residues: 78
  loop : -0.47 (0.47), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 858 
 HIS   0.002   0.001   HIS A 288 
 PHE   0.017   0.001   PHE A 897 
 TYR   0.028   0.002   TYR A 881 
 ARG   0.008   0.000   ARG A 761 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04275 (  461)
  hydrogen bonds       : angle       4.44503 ( 1401)
  SS BOND              : bond        0.00027 (    1)
  SS BOND              : angle       0.09124 (    2)
  covalent geometry    : bond        0.00338 ( 6852)
  covalent geometry    : angle       0.60144 ( 9283)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 153
  time to evaluate  : 0.699 
Fit side-chains
REVERT: A  137 HIS cc_start: 0.6776 (m90) cc_final: 0.6529 (m170)
REVERT: A  152 PHE cc_start: 0.5682 (t80) cc_final: 0.5398 (t80)
REVERT: A  240 LEU cc_start: 0.7709 (mm) cc_final: 0.7475 (mt)
REVERT: A  305 ARG cc_start: 0.7250 (mtt90) cc_final: 0.6997 (mmt-90)
REVERT: A  406 MET cc_start: 0.3955 (OUTLIER) cc_final: 0.3665 (mtm)
REVERT: A  448 VAL cc_start: 0.7844 (t) cc_final: 0.7605 (p)
REVERT: A  499 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8289 (mm)
REVERT: A  512 ASN cc_start: 0.6131 (OUTLIER) cc_final: 0.5633 (t0)
REVERT: A 1094 GLU cc_start: 0.6421 (tm-30) cc_final: 0.6040 (tm-30)
REVERT: A 1106 LYS cc_start: 0.7010 (OUTLIER) cc_final: 0.6457 (ptmm)
REVERT: A 1162 LYS cc_start: 0.6989 (OUTLIER) cc_final: 0.6424 (pttt)
REVERT: A 1213 TYR cc_start: 0.4297 (m-80) cc_final: 0.4055 (m-10)
  outliers start: 31
  outliers final: 23
  residues processed: 171
  average time/residue: 0.2303
  time to fit residues: 52.2489
Evaluate side-chains
  179 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 151
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 MET
Chi-restraints excluded: chain A residue  176 SER
Chi-restraints excluded: chain A residue  227 CYS
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  319 HIS
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  446 TYR
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  499 ILE
Chi-restraints excluded: chain A residue  500 LEU
Chi-restraints excluded: chain A residue  510 TRP
Chi-restraints excluded: chain A residue  512 ASN
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  531 ILE
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  784 THR
Chi-restraints excluded: chain A residue  849 MET
Chi-restraints excluded: chain A residue  866 HIS
Chi-restraints excluded: chain A residue  875 LEU
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  991 LEU
Chi-restraints excluded: chain A residue 1032 LEU
Chi-restraints excluded: chain A residue 1106 LYS
Chi-restraints excluded: chain A residue 1162 LYS
Chi-restraints excluded: chain A residue 1202 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 72 optimal weight:    0.6980
   chunk 2 optimal weight:    3.9990
   chunk 18 optimal weight:    0.6980
   chunk 68 optimal weight:    6.9990
   chunk 21 optimal weight:    0.5980
   chunk 52 optimal weight:    3.9990
   chunk 69 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 77 optimal weight:    1.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1009 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.164506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.139374 restraints weight = 9827.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.143863 restraints weight = 5450.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.146898 restraints weight = 3711.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.3924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6655
moved from start:          0.3514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6853  Z= 0.174
  Angle     :  0.628  13.041   9285  Z= 0.314
  Chirality :  0.040   0.163   1064
  Planarity :  0.004   0.050   1159
  Dihedral  :  4.217  15.928    911
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 31.40 %
    Favored  : 63.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  1.66 (0.30), residues: 828
  helix:  1.99 (0.22), residues: 538
  sheet: -0.47 (0.59), residues: 78
  loop : -0.54 (0.46), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 858 
 HIS   0.003   0.001   HIS A 171 
 PHE   0.018   0.001   PHE A 897 
 TYR   0.030   0.002   TYR A 243 
 ARG   0.009   0.001   ARG A 761 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04425 (  461)
  hydrogen bonds       : angle       4.50576 ( 1401)
  SS BOND              : bond        0.00033 (    1)
  SS BOND              : angle       0.09948 (    2)
  covalent geometry    : bond        0.00385 ( 6852)
  covalent geometry    : angle       0.62766 ( 9283)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 163
  time to evaluate  : 0.715 
Fit side-chains
REVERT: A  137 HIS cc_start: 0.6791 (m90) cc_final: 0.6568 (m170)
REVERT: A  143 ILE cc_start: 0.6432 (OUTLIER) cc_final: 0.6216 (pt)
REVERT: A  152 PHE cc_start: 0.5725 (t80) cc_final: 0.5441 (t80)
REVERT: A  240 LEU cc_start: 0.7966 (mm) cc_final: 0.7756 (mt)
REVERT: A  244 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7996 (mm)
REVERT: A  305 ARG cc_start: 0.7315 (mtt90) cc_final: 0.7076 (mmt-90)
REVERT: A  406 MET cc_start: 0.4081 (OUTLIER) cc_final: 0.3787 (mtm)
REVERT: A  448 VAL cc_start: 0.7851 (t) cc_final: 0.7644 (p)
REVERT: A  465 MET cc_start: 0.6959 (OUTLIER) cc_final: 0.5518 (tpt)
REVERT: A  499 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8263 (mm)
REVERT: A  512 ASN cc_start: 0.6154 (OUTLIER) cc_final: 0.5657 (t0)
REVERT: A 1043 GLN cc_start: 0.6958 (tm-30) cc_final: 0.6706 (tp-100)
REVERT: A 1094 GLU cc_start: 0.6425 (tm-30) cc_final: 0.6038 (tm-30)
REVERT: A 1106 LYS cc_start: 0.7019 (OUTLIER) cc_final: 0.6483 (ptmm)
REVERT: A 1162 LYS cc_start: 0.7011 (OUTLIER) cc_final: 0.6458 (pttt)
  outliers start: 34
  outliers final: 23
  residues processed: 181
  average time/residue: 0.2117
  time to fit residues: 50.1577
Evaluate side-chains
  191 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 160
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 ILE
Chi-restraints excluded: chain A residue  145 MET
Chi-restraints excluded: chain A residue  176 SER
Chi-restraints excluded: chain A residue  227 CYS
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  319 HIS
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  446 TYR
Chi-restraints excluded: chain A residue  465 MET
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  499 ILE
Chi-restraints excluded: chain A residue  500 LEU
Chi-restraints excluded: chain A residue  510 TRP
Chi-restraints excluded: chain A residue  512 ASN
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  531 ILE
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  784 THR
Chi-restraints excluded: chain A residue  849 MET
Chi-restraints excluded: chain A residue  866 HIS
Chi-restraints excluded: chain A residue  875 LEU
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  991 LEU
Chi-restraints excluded: chain A residue 1032 LEU
Chi-restraints excluded: chain A residue 1106 LYS
Chi-restraints excluded: chain A residue 1162 LYS
Chi-restraints excluded: chain A residue 1202 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 57 optimal weight:    0.7980
   chunk 20 optimal weight:    0.8980
   chunk 1 optimal weight:    0.8980
   chunk 2 optimal weight:    0.7980
   chunk 70 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9990
   chunk 14 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 79 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1009 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.165046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.139826 restraints weight = 9861.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.144271 restraints weight = 5450.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.147380 restraints weight = 3718.964|
|-----------------------------------------------------------------------------|
r_work (final): 0.3937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6644
moved from start:          0.3584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6853  Z= 0.158
  Angle     :  0.626  13.688   9285  Z= 0.312
  Chirality :  0.040   0.162   1064
  Planarity :  0.004   0.050   1159
  Dihedral  :  4.203  15.931    911
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 31.40 %
    Favored  : 64.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  1.66 (0.30), residues: 828
  helix:  1.99 (0.22), residues: 538
  sheet: -0.51 (0.59), residues: 78
  loop : -0.53 (0.46), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 510 
 HIS   0.003   0.001   HIS A 171 
 PHE   0.016   0.001   PHE A1223 
 TYR   0.020   0.002   TYR A1213 
 ARG   0.010   0.001   ARG A 761 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04328 (  461)
  hydrogen bonds       : angle       4.48099 ( 1401)
  SS BOND              : bond        0.00023 (    1)
  SS BOND              : angle       0.10257 (    2)
  covalent geometry    : bond        0.00353 ( 6852)
  covalent geometry    : angle       0.62619 ( 9283)

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

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

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1656 Ramachandran restraints generated.
    828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 160
  time to evaluate  : 0.690 
Fit side-chains
REVERT: A  137 HIS cc_start: 0.6780 (m90) cc_final: 0.6541 (m170)
REVERT: A  143 ILE cc_start: 0.6444 (OUTLIER) cc_final: 0.6233 (pt)
REVERT: A  152 PHE cc_start: 0.5707 (t80) cc_final: 0.5415 (t80)
REVERT: A  240 LEU cc_start: 0.7995 (mm) cc_final: 0.7788 (mt)
REVERT: A  244 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7942 (mm)
REVERT: A  406 MET cc_start: 0.4007 (OUTLIER) cc_final: 0.3719 (mtm)
REVERT: A  448 VAL cc_start: 0.7864 (t) cc_final: 0.7637 (p)
REVERT: A  499 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8258 (mm)
REVERT: A  512 ASN cc_start: 0.6122 (OUTLIER) cc_final: 0.5611 (t0)
REVERT: A 1094 GLU cc_start: 0.6406 (tm-30) cc_final: 0.5998 (tm-30)
REVERT: A 1106 LYS cc_start: 0.7012 (OUTLIER) cc_final: 0.6230 (ptmm)
REVERT: A 1162 LYS cc_start: 0.7011 (OUTLIER) cc_final: 0.6467 (pttt)
  outliers start: 31
  outliers final: 23
  residues processed: 177
  average time/residue: 0.1976
  time to fit residues: 45.8951
Evaluate side-chains
  186 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 156
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 ILE
Chi-restraints excluded: chain A residue  145 MET
Chi-restraints excluded: chain A residue  176 SER
Chi-restraints excluded: chain A residue  227 CYS
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  319 HIS
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  406 MET
Chi-restraints excluded: chain A residue  446 TYR
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  499 ILE
Chi-restraints excluded: chain A residue  500 LEU
Chi-restraints excluded: chain A residue  510 TRP
Chi-restraints excluded: chain A residue  512 ASN
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  531 ILE
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  784 THR
Chi-restraints excluded: chain A residue  849 MET
Chi-restraints excluded: chain A residue  866 HIS
Chi-restraints excluded: chain A residue  875 LEU
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  991 LEU
Chi-restraints excluded: chain A residue 1032 LEU
Chi-restraints excluded: chain A residue 1106 LYS
Chi-restraints excluded: chain A residue 1162 LYS
Chi-restraints excluded: chain A residue 1202 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 80 optimal weight:    3.9990
   chunk 21 optimal weight:    0.6980
   chunk 77 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 64 optimal weight:    0.7980
   chunk 13 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 70 optimal weight:    0.6980
   chunk 4 optimal weight:    6.9990
   chunk 57 optimal weight:    1.9990
   chunk 68 optimal weight:    0.0870
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
** A 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1009 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.165624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.140674 restraints weight = 9820.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.145196 restraints weight = 5430.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.148152 restraints weight = 3664.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.3942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6629
moved from start:          0.3704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6853  Z= 0.146
  Angle     :  0.620  13.353   9285  Z= 0.308
  Chirality :  0.039   0.159   1064
  Planarity :  0.004   0.050   1159
  Dihedral  :  4.134  15.860    911
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 31.40 %
    Favored  : 64.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  1.66 (0.30), residues: 828
  helix:  2.01 (0.22), residues: 540
  sheet: -0.48 (0.58), residues: 78
  loop : -0.64 (0.46), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1187 
 HIS   0.003   0.001   HIS A 292 
 PHE   0.018   0.001   PHE A1223 
 TYR   0.021   0.002   TYR A1213 
 ARG   0.010   0.000   ARG A 761 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04212 (  461)
  hydrogen bonds       : angle       4.44746 ( 1401)
  SS BOND              : bond        0.00019 (    1)
  SS BOND              : angle       0.09962 (    2)
  covalent geometry    : bond        0.00325 ( 6852)
  covalent geometry    : angle       0.62002 ( 9283)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2718.56 seconds
wall clock time: 48 minutes 12.09 seconds (2892.09 seconds total)