Starting phenix.real_space_refine
on Thu Mar 13 06:49:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cr8_45854/03_2025/9cr8_45854.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cr8_45854/03_2025/9cr8_45854.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cr8_45854/03_2025/9cr8_45854.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cr8_45854/03_2025/9cr8_45854.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cr8_45854/03_2025/9cr8_45854.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cr8_45854/03_2025/9cr8_45854.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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      32      5.16       5
     C    5675      2.51       5
     N    1426      2.21       5
     O    1531      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8664
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 8430
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1087, 8430
          Classifications: {'peptide': 1087}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 27, 'TRANS': 1059}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "A"
      Number of atoms: 234
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 234
          Unusual residues: {'UPL': 15}
          Classifications: {'undetermined': 15}
          Link IDs: {None: 14}
          Unresolved non-hydrogen bonds: 276
          Unresolved non-hydrogen angles: 289
          Unresolved non-hydrogen dihedrals: 302
          Unresolved non-hydrogen chiralities: 13
  Time building chain proxies: 5.45, per 1000 atoms: 0.63
  Number of scatterers: 8664
  At special positions: 0
  Unit cell: (98.604, 119.52, 114.54, 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      32     16.00
     O    1531      8.00
     N    1426      7.00
     C    5675      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.23
  Conformation dependent library (CDL) restraints added in 960.6 milliseconds
  

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2002

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 4 sheets defined
      66.1% alpha, 4.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.84
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 63
    Processing helix  chain 'A' and resid 64 through 81
      removed outlier: 3.518A  pdb=" N   ASN A  81 " --> pdb=" O   ASP A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 156
      removed outlier: 3.521A  pdb=" N   VAL A 133 " --> pdb=" O   ALA A 129 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   TRP A 136 " --> pdb=" O   GLN A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 164
      removed outlier: 3.667A  pdb=" N   PHE A 163 " --> pdb=" O   GLU A 159 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ASP A 164 " --> pdb=" O   ILE A 160 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 159 through 164'
    Processing helix  chain 'A' and resid 167 through 186
      removed outlier: 4.383A  pdb=" N   VAL A 179 " --> pdb=" O   LEU A 175 " (cutoff:3.500A)
      removed outlier: 4.266A  pdb=" N   SER A 180 " --> pdb=" O   THR A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 210
      removed outlier: 3.884A  pdb=" N   THR A 202 " --> pdb=" O   ALA A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 222
      removed outlier: 3.992A  pdb=" N   THR A 215 " --> pdb=" O   GLY A 211 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ALA A 220 " --> pdb=" O   LEU A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 241
      removed outlier: 3.699A  pdb=" N   LEU A 227 " --> pdb=" O   PRO A 223 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   ASP A 241 " --> pdb=" O   SER A 237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 260
    Processing helix  chain 'A' and resid 260 through 268
    Processing helix  chain 'A' and resid 269 through 315
    Processing helix  chain 'A' and resid 329 through 345
      removed outlier: 4.161A  pdb=" N   VAL A 338 " --> pdb=" O   VAL A 334 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   VAL A 345 " --> pdb=" O   GLY A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 348 through 371
      removed outlier: 3.946A  pdb=" N   GLU A 364 " --> pdb=" O   GLY A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 434 through 441
      removed outlier: 3.669A  pdb=" N   GLN A 441 " --> pdb=" O   VAL A 437 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 461
      No H-bonds generated for 'chain 'A' and resid 459 through 461'
    Processing helix  chain 'A' and resid 462 through 467
    Processing helix  chain 'A' and resid 468 through 470
      No H-bonds generated for 'chain 'A' and resid 468 through 470'
    Processing helix  chain 'A' and resid 483 through 490
    Processing helix  chain 'A' and resid 496 through 506
      removed outlier: 3.526A  pdb=" N   ILE A 500 " --> pdb=" O   THR A 496 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 509 through 516
    Processing helix  chain 'A' and resid 532 through 548
    Processing helix  chain 'A' and resid 565 through 578
      removed outlier: 3.554A  pdb=" N   VAL A 569 " --> pdb=" O   SER A 565 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   LYS A 578 " --> pdb=" O   ASP A 574 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 699 through 703
    Processing helix  chain 'A' and resid 707 through 736
      removed outlier: 3.633A  pdb=" N   PHE A 711 " --> pdb=" O   GLU A 707 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   GLN A 725 " --> pdb=" O   ASN A 721 " (cutoff:3.500A)
      Proline residue:  A 726  - end of helix
      removed outlier: 3.813A  pdb=" N   ALA A 729 " --> pdb=" O   GLN A 725 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ILE A 730 " --> pdb=" O   PRO A 726 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 737 through 739
      No H-bonds generated for 'chain 'A' and resid 737 through 739'
    Processing helix  chain 'A' and resid 752 through 799
    Processing helix  chain 'A' and resid 800 through 806
      removed outlier: 3.952A  pdb=" N   PHE A 804 " --> pdb=" O   ASP A 800 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 810 through 820
    Processing helix  chain 'A' and resid 825 through 854
      removed outlier: 4.229A  pdb=" N   LEU A 833 " --> pdb=" O   ILE A 829 " (cutoff:3.500A)
      removed outlier: 4.512A  pdb=" N   ALA A 834 " --> pdb=" O   GLY A 830 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   THR A 845 " --> pdb=" O   ALA A 841 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   GLY A 846 " --> pdb=" O   ASN A 842 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 855 through 890
      Proline residue:  A 866  - end of helix
      removed outlier: 3.683A  pdb=" N   GLN A 882 " --> pdb=" O   MET A 878 " (cutoff:3.500A)
      removed outlier: 4.751A  pdb=" N   LYS A 887 " --> pdb=" O   ALA A 883 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   LYS A 888 " --> pdb=" O   LEU A 884 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 891 through 903
    Processing helix  chain 'A' and resid 903 through 911
    Processing helix  chain 'A' and resid 912 through 965
      removed outlier: 3.619A  pdb=" N   PHE A 916 " --> pdb=" O   GLN A 912 " (cutoff:3.500A)
      Proline residue:  A 927  - end of helix
      removed outlier: 3.603A  pdb=" N   ALA A 935 " --> pdb=" O   SER A 931 " (cutoff:3.500A)
      removed outlier: 4.605A  pdb=" N   HIS A 936 " --> pdb=" O   LEU A 932 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   ILE A 937 " --> pdb=" O   ARG A 933 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   TYR A 953 " --> pdb=" O   MET A 949 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ALA A 954 " --> pdb=" O   TYR A 950 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 970 through 994
      removed outlier: 3.915A  pdb=" N   PHE A 983 " --> pdb=" O   SER A 979 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   ALA A 987 " --> pdb=" O   PHE A 983 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   SER A 993 " --> pdb=" O   GLY A 989 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   PHE A 994 " --> pdb=" O   GLN A 990 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 999 through 1012
      removed outlier: 3.825A  pdb=" N   ILE A1003 " --> pdb=" O   ALA A 999 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1078 through 1084
    Processing helix  chain 'A' and resid 1105 through 1111
    Processing helix  chain 'A' and resid 1126 through 1133
    Processing helix  chain 'A' and resid 1141 through 1152
      removed outlier: 3.799A  pdb=" N   ILE A1145 " --> pdb=" O   SER A1141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1154 through 1161
    Processing helix  chain 'A' and resid 1177 through 1193
      removed outlier: 3.951A  pdb=" N   ARG A1192 " --> pdb=" O   ARG A1188 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   GLN A1193 " --> pdb=" O   ALA A1189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1210 through 1222
      removed outlier: 3.572A  pdb=" N   VAL A1214 " --> pdb=" O   SER A1210 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 408 through 416
      removed outlier: 6.868A  pdb=" N   ILE A 409 " --> pdb=" O   SER A 400 " (cutoff:3.500A)
      removed outlier: 7.439A  pdb=" N   SER A 400 " --> pdb=" O   ILE A 409 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   LYS A 411 " --> pdb=" O   HIS A 398 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   HIS A 398 " --> pdb=" O   LYS A 411 " (cutoff:3.500A)
      removed outlier: 5.126A  pdb=" N   LEU A 413 " --> pdb=" O   ASN A 396 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   SER A 452 " --> pdb=" O   GLU A 393 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 551 through 552
      removed outlier: 3.751A  pdb=" N   ALA A 599 " --> pdb=" O   ALA A 424 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1035 through 1041
      removed outlier: 5.524A  pdb=" N   PHE A1037 " --> pdb=" O   LEU A1095 " (cutoff:3.500A)
      removed outlier: 7.084A  pdb=" N   LEU A1095 " --> pdb=" O   PHE A1037 " (cutoff:3.500A)
      removed outlier: 5.305A  pdb=" N   GLU A1039 " --> pdb=" O   LYS A1093 " (cutoff:3.500A)
      removed outlier: 4.850A  pdb=" N   LYS A1093 " --> pdb=" O   GLU A1039 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1065 through 1067
      removed outlier: 6.358A  pdb=" N   LEU A1066 " --> pdb=" O   VAL A1229 " (cutoff:3.500A)

    521 hydrogen bonds defined for protein.
    1539 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: 2.92

  Time building geometry restraints manager: 2.62 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: 2715
        1.34 -     1.46: 1818
        1.46 -     1.58: 4216
        1.58 -     1.69: 0
        1.69 -     1.81: 57
  Bond restraints: 8806
  Sorted by residual:
  bond pdb=" N   VAL A  71 "
       pdb=" CA  VAL A  71 "
    ideal  model  delta    sigma   weight residual
    1.460  1.495 -0.035 1.21e-02 6.83e+03 8.47e+00
  bond pdb=" N   ILE A  78 "
       pdb=" CA  ILE A  78 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.034 1.19e-02 7.06e+03 8.05e+00
  bond pdb=" N   GLU A  74 "
       pdb=" CA  GLU A  74 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.19e-02 7.06e+03 6.20e+00
  bond pdb=" N   ASP A 188 "
       pdb=" CA  ASP A 188 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.033 1.31e-02 5.83e+03 6.18e+00
  bond pdb=" N   THR A  76 "
       pdb=" CA  THR A  76 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.21e-02 6.83e+03 6.06e+00
  ... (remaining 8801 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.27: 11492
        1.27 -     2.54: 253
        2.54 -     3.82: 59
        3.82 -     5.09: 10
        5.09 -     6.36: 2
  Bond angle restraints: 11816
  Sorted by residual:
  angle pdb=" C   ALA A 246 "
        pdb=" N   TYR A 247 "
        pdb=" CA  TYR A 247 "
      ideal   model   delta    sigma   weight residual
     120.72  114.62    6.10 1.67e+00 3.59e-01 1.33e+01
  angle pdb=" CA  VAL A  71 "
        pdb=" C   VAL A  71 "
        pdb=" O   VAL A  71 "
      ideal   model   delta    sigma   weight residual
     120.85  117.14    3.71 1.06e+00 8.90e-01 1.23e+01
  angle pdb=" CA  ILE A  78 "
        pdb=" C   ILE A  78 "
        pdb=" O   ILE A  78 "
      ideal   model   delta    sigma   weight residual
     120.95  117.86    3.09 1.04e+00 9.25e-01 8.80e+00
  angle pdb=" CA  GLY A  73 "
        pdb=" C   GLY A  73 "
        pdb=" O   GLY A  73 "
      ideal   model   delta    sigma   weight residual
     120.75  117.69    3.06 1.03e+00 9.43e-01 8.80e+00
  angle pdb=" CA  MET A  75 "
        pdb=" C   MET A  75 "
        pdb=" O   MET A  75 "
      ideal   model   delta    sigma   weight residual
     120.55  117.42    3.13 1.06e+00 8.90e-01 8.70e+00
  ... (remaining 11811 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.31: 4867
       17.31 -    34.62: 331
       34.62 -    51.94: 86
       51.94 -    69.25: 15
       69.25 -    86.56: 4
  Dihedral angle restraints: 5303
    sinusoidal: 2184
      harmonic: 3119
  Sorted by residual:
  dihedral pdb=" CA  ASP A 821 "
           pdb=" C   ASP A 821 "
           pdb=" N   ALA A 822 "
           pdb=" CA  ALA A 822 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.19   17.81     0      5.00e+00 4.00e-02 1.27e+01
  dihedral pdb=" CA  PHE A 983 "
           pdb=" C   PHE A 983 "
           pdb=" N   GLY A 984 "
           pdb=" CA  GLY A 984 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.28   17.72     0      5.00e+00 4.00e-02 1.26e+01
  dihedral pdb=" CA  PHE A 697 "
           pdb=" C   PHE A 697 "
           pdb=" N   TRP A 698 "
           pdb=" CA  TRP A 698 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.21   16.79     0      5.00e+00 4.00e-02 1.13e+01
  ... (remaining 5300 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 940
       0.035 -    0.070: 301
       0.070 -    0.104: 72
       0.104 -    0.139: 31
       0.139 -    0.174: 4
  Chirality restraints: 1348
  Sorted by residual:
  chirality pdb=" CB  VAL A  71 "
            pdb=" CA  VAL A  71 "
            pdb=" CG1 VAL A  71 "
            pdb=" CG2 VAL A  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.17 2.00e-01 2.50e+01 7.55e-01
  chirality pdb=" CA  ILE A  78 "
            pdb=" N   ILE A  78 "
            pdb=" C   ILE A  78 "
            pdb=" CB  ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.00e-01
  chirality pdb=" CA  LEU A  70 "
            pdb=" N   LEU A  70 "
            pdb=" C   LEU A  70 "
            pdb=" CB  LEU A  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.23e-01
  ... (remaining 1345 not shown)

  Planarity restraints: 1465
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 980 "    0.009 2.00e-02 2.50e+03   1.71e-02 2.92e+00
        pdb=" C   ALA A 980 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   ALA A 980 "    0.011 2.00e-02 2.50e+03
        pdb=" N   VAL A 981 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 222 "   -0.028 5.00e-02 4.00e+02   4.21e-02 2.83e+00
        pdb=" N   PRO A 223 "    0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO A 223 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 223 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 203 "    0.008 2.00e-02 2.50e+03   1.68e-02 2.82e+00
        pdb=" C   GLY A 203 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   GLY A 203 "    0.011 2.00e-02 2.50e+03
        pdb=" N   PHE A 204 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1462 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1235
        2.76 -     3.29: 8760
        3.29 -     3.83: 13591
        3.83 -     4.36: 15059
        4.36 -     4.90: 26804
  Nonbonded interactions: 65449
  Sorted by model distance:
  nonbonded pdb=" O   HIS A 398 "
            pdb=" OG1 THR A 447 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" O   LEU A 216 "
            pdb=" OH  TYR A 310 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" O   ASP A 805 "
            pdb=" OD1 ASP A 805 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" NH1 ARG A 588 "
            pdb=" OG  SER A 590 "
     model   vdw
     2.274 3.120
  nonbonded pdb=" OE2 GLU A 273 "
            pdb=" OH  TYR A1133 "
     model   vdw
     2.280 3.040
  ... (remaining 65444 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:             1.000
  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:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     23.070
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7508
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      :  0.003   0.035   8806  Z= 0.174
  Angle     :  0.494   6.359  11816  Z= 0.295
  Chirality :  0.039   0.174   1348
  Planarity :  0.004   0.042   1465
  Dihedral  : 12.788  86.561   3301
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  9.43 %
    Favored  : 90.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.26), residues: 1081
  helix:  1.47 (0.20), residues: 678
  sheet: -0.80 (0.82), residues: 52
  loop : -1.85 (0.32), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 698 
 HIS   0.002   0.001   HIS A1007 
 PHE   0.011   0.001   PHE A  72 
 TYR   0.021   0.001   TYR A 247 
 ARG   0.002   0.000   ARG A 699 

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 167
  time to evaluate  : 0.927 
Fit side-chains
REVERT: A   75 MET cc_start: 0.6481 (ttt) cc_final: 0.5567 (mtp)
REVERT: A  380 LYS cc_start: 0.7684 (ptpp) cc_final: 0.6619 (ttpt)
REVERT: A  450 MET cc_start: 0.7276 (ptp) cc_final: 0.6916 (ptp)
REVERT: A  460 THR cc_start: 0.7788 (p) cc_final: 0.7358 (p)
REVERT: A  502 LYS cc_start: 0.8239 (mtpp) cc_final: 0.7907 (ttmm)
REVERT: A  925 GLN cc_start: 0.7926 (tm-30) cc_final: 0.7178 (tt0)
REVERT: A  950 TYR cc_start: 0.7373 (t80) cc_final: 0.7171 (t80)
REVERT: A  951 PHE cc_start: 0.7243 (t80) cc_final: 0.6832 (t80)
REVERT: A  974 VAL cc_start: 0.8699 (t) cc_final: 0.8364 (t)
REVERT: A 1062 LYS cc_start: 0.6913 (tptt) cc_final: 0.6088 (tttt)
REVERT: A 1172 LYS cc_start: 0.6659 (pttt) cc_final: 0.6425 (pttp)
  outliers start: 2
  outliers final: 1
  residues processed: 168
  average time/residue: 0.2034
  time to fit residues: 47.3449
Evaluate side-chains
  123 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 122
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  535 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    0.8980
   chunk 81 optimal weight:    0.9990
   chunk 45 optimal weight:    6.9990
   chunk 27 optimal weight:    0.0470
   chunk 55 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   chunk 84 optimal weight:    0.0270
   chunk 32 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 63 optimal weight:    3.9990
   chunk 98 optimal weight:    2.9990
   overall best weight:    0.7940

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

Flipped N/Q/H residues before XYZ refinement:
A 330 GLN
A 487 ASN
A 530 GLN
A 535 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.177256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.149446 restraints weight = 12369.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.147055 restraints weight = 14923.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.148732 restraints weight = 15438.117|
|-----------------------------------------------------------------------------|
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7561
moved from start:          0.1286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   8806  Z= 0.167
  Angle     :  0.504   6.496  11816  Z= 0.274
  Chirality :  0.039   0.149   1348
  Planarity :  0.003   0.040   1465
  Dihedral  :  7.393  58.673   1364
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.92 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 14.14 %
    Favored  : 83.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.26), residues: 1081
  helix:  1.90 (0.20), residues: 684
  sheet: -1.19 (0.73), residues: 62
  loop : -1.80 (0.33), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 698 
 HIS   0.002   0.001   HIS A 153 
 PHE   0.019   0.001   PHE A  72 
 TYR   0.043   0.002   TYR A 998 
 ARG   0.003   0.000   ARG A 467 

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 135
  time to evaluate  : 0.833 
Fit side-chains
REVERT: A  380 LYS cc_start: 0.7559 (ptpp) cc_final: 0.6753 (ttpt)
REVERT: A  925 GLN cc_start: 0.7636 (tm-30) cc_final: 0.7022 (tt0)
REVERT: A  951 PHE cc_start: 0.7087 (t80) cc_final: 0.6752 (t80)
REVERT: A 1062 LYS cc_start: 0.6734 (tptt) cc_final: 0.6209 (tttt)
  outliers start: 23
  outliers final: 16
  residues processed: 148
  average time/residue: 0.1925
  time to fit residues: 41.0581
Evaluate side-chains
  131 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 115
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  487 ASN
Chi-restraints excluded: chain A residue  535 GLN
Chi-restraints excluded: chain A residue  811 THR
Chi-restraints excluded: chain A residue  911 THR
Chi-restraints excluded: chain A residue  963 LEU
Chi-restraints excluded: chain A residue  971 PHE
Chi-restraints excluded: chain A residue 1010 MET
Chi-restraints excluded: chain A residue 1050 ILE
Chi-restraints excluded: chain A residue 1058 LEU
Chi-restraints excluded: chain A residue 1065 THR
Chi-restraints excluded: chain A residue 1078 THR
Chi-restraints excluded: chain A residue 1083 LEU
Chi-restraints excluded: chain A residue 1084 GLU
Chi-restraints excluded: chain A residue 1121 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 84 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0370
   chunk 11 optimal weight:    0.7980
   chunk 43 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   chunk 57 optimal weight:    7.9990
   chunk 106 optimal weight:    8.9990
   chunk 2 optimal weight:    0.9990
   chunk 52 optimal weight:    7.9990
   overall best weight:    0.9262

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

Flipped N/Q/H residues before XYZ refinement:
A 587 HIS
A 750 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.179596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.155489 restraints weight = 12692.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.153565 restraints weight = 20123.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.152899 restraints weight = 16771.440|
|-----------------------------------------------------------------------------|
r_work (final): 0.3774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.1689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   8806  Z= 0.173
  Angle     :  0.501   6.564  11816  Z= 0.272
  Chirality :  0.038   0.144   1348
  Planarity :  0.003   0.040   1465
  Dihedral  :  7.376  59.809   1364
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 14.03 %
    Favored  : 82.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.26), residues: 1081
  helix:  1.98 (0.20), residues: 685
  sheet: -1.28 (0.72), residues: 62
  loop : -1.86 (0.32), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 315 
 HIS   0.002   0.001   HIS A1007 
 PHE   0.009   0.001   PHE A 767 
 TYR   0.034   0.002   TYR A 998 
 ARG   0.008   0.000   ARG A1147 

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 124
  time to evaluate  : 0.989 
Fit side-chains
REVERT: A  380 LYS cc_start: 0.7642 (ptpp) cc_final: 0.6728 (ttpt)
REVERT: A  925 GLN cc_start: 0.7690 (tm-30) cc_final: 0.7072 (tt0)
REVERT: A  934 LYS cc_start: 0.7716 (OUTLIER) cc_final: 0.7408 (tttm)
REVERT: A 1062 LYS cc_start: 0.6618 (tptt) cc_final: 0.6163 (tttt)
  outliers start: 32
  outliers final: 23
  residues processed: 144
  average time/residue: 0.1929
  time to fit residues: 40.1804
Evaluate side-chains
  138 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 114
  time to evaluate  : 1.020 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  117 TYR
Chi-restraints excluded: chain A residue  188 ASP
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  535 GLN
Chi-restraints excluded: chain A residue  700 ILE
Chi-restraints excluded: chain A residue  756 SER
Chi-restraints excluded: chain A residue  811 THR
Chi-restraints excluded: chain A residue  856 GLN
Chi-restraints excluded: chain A residue  898 THR
Chi-restraints excluded: chain A residue  911 THR
Chi-restraints excluded: chain A residue  913 GLU
Chi-restraints excluded: chain A residue  934 LYS
Chi-restraints excluded: chain A residue  963 LEU
Chi-restraints excluded: chain A residue  971 PHE
Chi-restraints excluded: chain A residue 1036 THR
Chi-restraints excluded: chain A residue 1050 ILE
Chi-restraints excluded: chain A residue 1058 LEU
Chi-restraints excluded: chain A residue 1065 THR
Chi-restraints excluded: chain A residue 1078 THR
Chi-restraints excluded: chain A residue 1083 LEU
Chi-restraints excluded: chain A residue 1084 GLU
Chi-restraints excluded: chain A residue 1121 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9980
   chunk 74 optimal weight:    6.9990
   chunk 18 optimal weight:    6.9990
   chunk 52 optimal weight:    6.9990
   chunk 91 optimal weight:    6.9990
   chunk 62 optimal weight:    0.8980
   chunk 40 optimal weight:    6.9990
   chunk 69 optimal weight:    0.6980
   chunk 97 optimal weight:    1.9990
   chunk 76 optimal weight:    0.8980
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
A 330 GLN
** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1175 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.178706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.152628 restraints weight = 12613.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.150521 restraints weight = 16369.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.152468 restraints weight = 16485.223|
|-----------------------------------------------------------------------------|
r_work (final): 0.3772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7600
moved from start:          0.1976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8806  Z= 0.188
  Angle     :  0.504   7.511  11816  Z= 0.273
  Chirality :  0.039   0.146   1348
  Planarity :  0.003   0.040   1465
  Dihedral  :  7.473  54.707   1364
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 15.71 %
    Favored  : 80.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.26), residues: 1081
  helix:  1.94 (0.20), residues: 685
  sheet: -1.26 (0.71), residues: 62
  loop : -1.86 (0.32), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 315 
 HIS   0.002   0.001   HIS A 518 
 PHE   0.020   0.001   PHE A1157 
 TYR   0.028   0.002   TYR A 247 
 ARG   0.004   0.000   ARG A1147 

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 117
  time to evaluate  : 0.825 
Fit side-chains
REVERT: A   75 MET cc_start: 0.6328 (ttt) cc_final: 0.5636 (mtp)
REVERT: A  315 TRP cc_start: 0.6739 (OUTLIER) cc_final: 0.5982 (t60)
REVERT: A  736 ILE cc_start: 0.8415 (tp) cc_final: 0.8142 (tp)
REVERT: A  925 GLN cc_start: 0.7692 (tm-30) cc_final: 0.7103 (tt0)
REVERT: A  934 LYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7520 (tttm)
REVERT: A  986 MET cc_start: 0.7548 (mtp) cc_final: 0.7321 (mtm)
REVERT: A 1062 LYS cc_start: 0.6752 (tptt) cc_final: 0.6148 (tttt)
  outliers start: 34
  outliers final: 26
  residues processed: 141
  average time/residue: 0.1710
  time to fit residues: 35.3480
Evaluate side-chains
  142 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 114
  time to evaluate  : 0.842 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 TYR
Chi-restraints excluded: chain A residue  188 ASP
Chi-restraints excluded: chain A residue  239 PHE
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  315 TRP
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain A residue  535 GLN
Chi-restraints excluded: chain A residue  756 SER
Chi-restraints excluded: chain A residue  811 THR
Chi-restraints excluded: chain A residue  856 GLN
Chi-restraints excluded: chain A residue  898 THR
Chi-restraints excluded: chain A residue  911 THR
Chi-restraints excluded: chain A residue  913 GLU
Chi-restraints excluded: chain A residue  918 HIS
Chi-restraints excluded: chain A residue  934 LYS
Chi-restraints excluded: chain A residue  971 PHE
Chi-restraints excluded: chain A residue 1010 MET
Chi-restraints excluded: chain A residue 1036 THR
Chi-restraints excluded: chain A residue 1050 ILE
Chi-restraints excluded: chain A residue 1058 LEU
Chi-restraints excluded: chain A residue 1065 THR
Chi-restraints excluded: chain A residue 1078 THR
Chi-restraints excluded: chain A residue 1083 LEU
Chi-restraints excluded: chain A residue 1121 ILE
Chi-restraints excluded: chain A residue 1190 LEU
Chi-restraints excluded: chain A residue 1213 VAL
Chi-restraints excluded: chain A residue 1230 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 51 optimal weight:    0.6980
   chunk 33 optimal weight:    0.4980
   chunk 65 optimal weight:    0.9980
   chunk 54 optimal weight:   20.0000
   chunk 4 optimal weight:    6.9990
   chunk 12 optimal weight:    0.6980
   chunk 100 optimal weight:    3.9990
   chunk 93 optimal weight:    6.9990
   chunk 102 optimal weight:    6.9990
   chunk 76 optimal weight:    2.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A 508 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 = 0.4090 r_free = 0.4090 target = 0.179765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.156355 restraints weight = 12557.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.154346 restraints weight = 20734.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.155041 restraints weight = 18325.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.3806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7544
moved from start:          0.2086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8806  Z= 0.158
  Angle     :  0.484   8.996  11816  Z= 0.263
  Chirality :  0.038   0.141   1348
  Planarity :  0.003   0.040   1465
  Dihedral  :  7.317  57.574   1364
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 16.50 %
    Favored  : 79.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.26), residues: 1081
  helix:  2.00 (0.20), residues: 691
  sheet: -0.75 (0.78), residues: 52
  loop : -2.07 (0.31), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 315 
 HIS   0.002   0.000   HIS A 166 
 PHE   0.017   0.001   PHE A1157 
 TYR   0.026   0.002   TYR A 247 
 ARG   0.004   0.000   ARG A1147 

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 122
  time to evaluate  : 1.029 
Fit side-chains
   revert: symmetry clash
REVERT: A  315 TRP cc_start: 0.6736 (OUTLIER) cc_final: 0.5993 (t60)
REVERT: A  851 PHE cc_start: 0.5520 (OUTLIER) cc_final: 0.5319 (m-10)
REVERT: A  925 GLN cc_start: 0.7646 (tm-30) cc_final: 0.7057 (tt0)
REVERT: A  934 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.7460 (tttm)
REVERT: A  986 MET cc_start: 0.7529 (mtp) cc_final: 0.7324 (mtm)
REVERT: A 1062 LYS cc_start: 0.6663 (tptt) cc_final: 0.6131 (tttt)
  outliers start: 36
  outliers final: 26
  residues processed: 149
  average time/residue: 0.2595
  time to fit residues: 56.8235
Evaluate side-chains
  142 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 113
  time to evaluate  : 1.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 TYR
Chi-restraints excluded: chain A residue  188 ASP
Chi-restraints excluded: chain A residue  239 PHE
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  315 TRP
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain A residue  535 GLN
Chi-restraints excluded: chain A residue  756 SER
Chi-restraints excluded: chain A residue  808 LYS
Chi-restraints excluded: chain A residue  811 THR
Chi-restraints excluded: chain A residue  851 PHE
Chi-restraints excluded: chain A residue  856 GLN
Chi-restraints excluded: chain A residue  911 THR
Chi-restraints excluded: chain A residue  913 GLU
Chi-restraints excluded: chain A residue  918 HIS
Chi-restraints excluded: chain A residue  934 LYS
Chi-restraints excluded: chain A residue 1010 MET
Chi-restraints excluded: chain A residue 1036 THR
Chi-restraints excluded: chain A residue 1050 ILE
Chi-restraints excluded: chain A residue 1058 LEU
Chi-restraints excluded: chain A residue 1065 THR
Chi-restraints excluded: chain A residue 1078 THR
Chi-restraints excluded: chain A residue 1083 LEU
Chi-restraints excluded: chain A residue 1084 GLU
Chi-restraints excluded: chain A residue 1121 ILE
Chi-restraints excluded: chain A residue 1190 LEU
Chi-restraints excluded: chain A residue 1213 VAL
Chi-restraints excluded: chain A residue 1230 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 90 optimal weight:    0.0870
   chunk 46 optimal weight:    9.9990
   chunk 105 optimal weight:    0.3980
   chunk 22 optimal weight:    0.7980
   chunk 88 optimal weight:    4.9990
   chunk 19 optimal weight:    0.7980
   chunk 107 optimal weight:    3.9990
   chunk 106 optimal weight:    7.9990
   chunk 74 optimal weight:    6.9990
   chunk 84 optimal weight:    0.5980
   chunk 51 optimal weight:    0.7980
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
** A 508 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 = 0.4112 r_free = 0.4112 target = 0.181813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.157879 restraints weight = 12493.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.156393 restraints weight = 17939.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.157669 restraints weight = 16416.910|
|-----------------------------------------------------------------------------|
r_work (final): 0.3840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7494
moved from start:          0.2221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   8806  Z= 0.139
  Angle     :  0.469   9.807  11816  Z= 0.255
  Chirality :  0.038   0.154   1348
  Planarity :  0.003   0.039   1465
  Dihedral  :  7.066  59.812   1364
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.92 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 18.74 %
    Favored  : 77.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.26), residues: 1081
  helix:  2.12 (0.20), residues: 693
  sheet: -0.57 (0.78), residues: 52
  loop : -2.06 (0.31), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 315 
 HIS   0.002   0.000   HIS A1155 
 PHE   0.026   0.001   PHE A1157 
 TYR   0.025   0.001   TYR A 247 
 ARG   0.001   0.000   ARG A 467 

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 124
  time to evaluate  : 0.759 
Fit side-chains
   revert: symmetry clash
REVERT: A  117 TYR cc_start: 0.7886 (OUTLIER) cc_final: 0.6540 (t80)
REVERT: A  315 TRP cc_start: 0.6713 (OUTLIER) cc_final: 0.5980 (t60)
REVERT: A  736 ILE cc_start: 0.8348 (tp) cc_final: 0.7891 (tp)
REVERT: A  851 PHE cc_start: 0.5502 (OUTLIER) cc_final: 0.5238 (m-10)
REVERT: A  925 GLN cc_start: 0.7477 (tm-30) cc_final: 0.6899 (tt0)
REVERT: A  934 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7431 (tttm)
REVERT: A 1062 LYS cc_start: 0.6435 (tptt) cc_final: 0.6014 (tttt)
  outliers start: 30
  outliers final: 21
  residues processed: 145
  average time/residue: 0.2053
  time to fit residues: 42.9197
Evaluate side-chains
  139 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 114
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 TYR
Chi-restraints excluded: chain A residue  188 ASP
Chi-restraints excluded: chain A residue  239 PHE
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  315 TRP
Chi-restraints excluded: chain A residue  535 GLN
Chi-restraints excluded: chain A residue  756 SER
Chi-restraints excluded: chain A residue  808 LYS
Chi-restraints excluded: chain A residue  811 THR
Chi-restraints excluded: chain A residue  851 PHE
Chi-restraints excluded: chain A residue  856 GLN
Chi-restraints excluded: chain A residue  898 THR
Chi-restraints excluded: chain A residue  911 THR
Chi-restraints excluded: chain A residue  913 GLU
Chi-restraints excluded: chain A residue  918 HIS
Chi-restraints excluded: chain A residue  934 LYS
Chi-restraints excluded: chain A residue 1010 MET
Chi-restraints excluded: chain A residue 1050 ILE
Chi-restraints excluded: chain A residue 1058 LEU
Chi-restraints excluded: chain A residue 1078 THR
Chi-restraints excluded: chain A residue 1083 LEU
Chi-restraints excluded: chain A residue 1121 ILE
Chi-restraints excluded: chain A residue 1213 VAL
Chi-restraints excluded: chain A residue 1230 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   chunk 58 optimal weight:    0.6980
   chunk 40 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9980
   chunk 63 optimal weight:    4.9990
   chunk 61 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   chunk 92 optimal weight:    7.9990
   chunk 90 optimal weight:    0.8980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 508 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 = 0.4095 r_free = 0.4095 target = 0.180270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.156657 restraints weight = 12655.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.155381 restraints weight = 17037.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.156172 restraints weight = 16587.469|
|-----------------------------------------------------------------------------|
r_work (final): 0.3820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7520
moved from start:          0.2341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8806  Z= 0.169
  Angle     :  0.511  10.653  11816  Z= 0.271
  Chirality :  0.039   0.151   1348
  Planarity :  0.003   0.038   1465
  Dihedral  :  7.153  58.184   1364
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 19.30 %
    Favored  : 76.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.26), residues: 1081
  helix:  2.01 (0.20), residues: 692
  sheet: -1.08 (0.71), residues: 62
  loop : -1.95 (0.32), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 315 
 HIS   0.002   0.000   HIS A 518 
 PHE   0.023   0.001   PHE A1157 
 TYR   0.027   0.002   TYR A 247 
 ARG   0.002   0.000   ARG A 467 

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 116
  time to evaluate  : 1.370 
Fit side-chains
REVERT: A  117 TYR cc_start: 0.7890 (OUTLIER) cc_final: 0.6537 (t80)
REVERT: A  315 TRP cc_start: 0.6743 (OUTLIER) cc_final: 0.6006 (t60)
REVERT: A  736 ILE cc_start: 0.8226 (tp) cc_final: 0.7836 (tp)
REVERT: A  851 PHE cc_start: 0.5554 (OUTLIER) cc_final: 0.5316 (m-10)
REVERT: A  925 GLN cc_start: 0.7503 (tm-30) cc_final: 0.6951 (tt0)
REVERT: A  934 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7477 (tttm)
REVERT: A 1062 LYS cc_start: 0.6720 (tptt) cc_final: 0.6231 (tttt)
  outliers start: 35
  outliers final: 24
  residues processed: 142
  average time/residue: 0.1915
  time to fit residues: 40.4685
Evaluate side-chains
  135 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 107
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 TYR
Chi-restraints excluded: chain A residue  188 ASP
Chi-restraints excluded: chain A residue  239 PHE
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  315 TRP
Chi-restraints excluded: chain A residue  535 GLN
Chi-restraints excluded: chain A residue  756 SER
Chi-restraints excluded: chain A residue  808 LYS
Chi-restraints excluded: chain A residue  811 THR
Chi-restraints excluded: chain A residue  851 PHE
Chi-restraints excluded: chain A residue  898 THR
Chi-restraints excluded: chain A residue  911 THR
Chi-restraints excluded: chain A residue  913 GLU
Chi-restraints excluded: chain A residue  918 HIS
Chi-restraints excluded: chain A residue  934 LYS
Chi-restraints excluded: chain A residue  963 LEU
Chi-restraints excluded: chain A residue 1010 MET
Chi-restraints excluded: chain A residue 1036 THR
Chi-restraints excluded: chain A residue 1050 ILE
Chi-restraints excluded: chain A residue 1058 LEU
Chi-restraints excluded: chain A residue 1065 THR
Chi-restraints excluded: chain A residue 1078 THR
Chi-restraints excluded: chain A residue 1083 LEU
Chi-restraints excluded: chain A residue 1121 ILE
Chi-restraints excluded: chain A residue 1190 LEU
Chi-restraints excluded: chain A residue 1213 VAL
Chi-restraints excluded: chain A residue 1230 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 80 optimal weight:    7.9990
   chunk 48 optimal weight:    0.8980
   chunk 78 optimal weight:    0.7980
   chunk 50 optimal weight:    0.0470
   chunk 63 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0570
   chunk 3 optimal weight:    1.9990
   chunk 103 optimal weight:    4.9990
   overall best weight:    0.7598

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

Flipped N/Q/H residues before XYZ refinement:
** A 508 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 = 0.4102 r_free = 0.4102 target = 0.180859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.153413 restraints weight = 12754.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.151104 restraints weight = 13553.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.151968 restraints weight = 13076.480|
|-----------------------------------------------------------------------------|
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.2414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8806  Z= 0.160
  Angle     :  0.511  11.427  11816  Z= 0.272
  Chirality :  0.039   0.247   1348
  Planarity :  0.003   0.038   1465
  Dihedral  :  7.141  58.210   1364
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 19.53 %
    Favored  : 76.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.06 (0.26), residues: 1081
  helix:  2.01 (0.20), residues: 693
  sheet: -0.48 (0.78), residues: 52
  loop : -2.01 (0.32), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 315 
 HIS   0.001   0.000   HIS A 518 
 PHE   0.026   0.001   PHE A1157 
 TYR   0.026   0.001   TYR A 247 
 ARG   0.002   0.000   ARG A 467 

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 113
  time to evaluate  : 0.832 
Fit side-chains
REVERT: A   75 MET cc_start: 0.6399 (ttt) cc_final: 0.5623 (mtp)
REVERT: A  117 TYR cc_start: 0.7988 (OUTLIER) cc_final: 0.6615 (t80)
REVERT: A  297 ILE cc_start: 0.8520 (tp) cc_final: 0.8308 (mt)
REVERT: A  315 TRP cc_start: 0.6710 (OUTLIER) cc_final: 0.5975 (t60)
REVERT: A  736 ILE cc_start: 0.8276 (tp) cc_final: 0.7951 (tp)
REVERT: A  851 PHE cc_start: 0.5555 (OUTLIER) cc_final: 0.5247 (m-10)
REVERT: A  925 GLN cc_start: 0.7449 (tm-30) cc_final: 0.6917 (tt0)
REVERT: A  934 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7473 (tttm)
REVERT: A 1062 LYS cc_start: 0.6749 (tptt) cc_final: 0.6138 (tttt)
  outliers start: 35
  outliers final: 24
  residues processed: 140
  average time/residue: 0.1808
  time to fit residues: 36.5617
Evaluate side-chains
  133 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 105
  time to evaluate  : 0.927 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 TYR
Chi-restraints excluded: chain A residue  132 GLN
Chi-restraints excluded: chain A residue  188 ASP
Chi-restraints excluded: chain A residue  239 PHE
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  315 TRP
Chi-restraints excluded: chain A residue  535 GLN
Chi-restraints excluded: chain A residue  808 LYS
Chi-restraints excluded: chain A residue  811 THR
Chi-restraints excluded: chain A residue  851 PHE
Chi-restraints excluded: chain A residue  856 GLN
Chi-restraints excluded: chain A residue  898 THR
Chi-restraints excluded: chain A residue  911 THR
Chi-restraints excluded: chain A residue  913 GLU
Chi-restraints excluded: chain A residue  918 HIS
Chi-restraints excluded: chain A residue  934 LYS
Chi-restraints excluded: chain A residue  963 LEU
Chi-restraints excluded: chain A residue 1010 MET
Chi-restraints excluded: chain A residue 1036 THR
Chi-restraints excluded: chain A residue 1050 ILE
Chi-restraints excluded: chain A residue 1065 THR
Chi-restraints excluded: chain A residue 1078 THR
Chi-restraints excluded: chain A residue 1083 LEU
Chi-restraints excluded: chain A residue 1121 ILE
Chi-restraints excluded: chain A residue 1190 LEU
Chi-restraints excluded: chain A residue 1213 VAL
Chi-restraints excluded: chain A residue 1230 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 64 optimal weight:    0.7980
   chunk 107 optimal weight:    1.9990
   chunk 84 optimal weight:    0.5980
   chunk 104 optimal weight:    0.8980
   chunk 36 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 98 optimal weight:    0.1980
   chunk 92 optimal weight:    0.1980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A 508 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 = 0.4111 r_free = 0.4111 target = 0.181865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.157687 restraints weight = 12610.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.156382 restraints weight = 16887.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.158646 restraints weight = 15805.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.3840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7492
moved from start:          0.2514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   8806  Z= 0.145
  Angle     :  0.517  10.999  11816  Z= 0.274
  Chirality :  0.039   0.199   1348
  Planarity :  0.003   0.038   1465
  Dihedral  :  7.002  59.404   1364
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 20.09 %
    Favored  : 76.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.26), residues: 1081
  helix:  2.07 (0.20), residues: 693
  sheet: -0.09 (0.87), residues: 42
  loop : -2.00 (0.32), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 315 
 HIS   0.001   0.000   HIS A 166 
 PHE   0.045   0.001   PHE A1157 
 TYR   0.043   0.001   TYR A 998 
 ARG   0.002   0.000   ARG A1085 

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 109
  time to evaluate  : 0.939 
Fit side-chains
REVERT: A   75 MET cc_start: 0.6344 (ttt) cc_final: 0.5657 (mtp)
REVERT: A  117 TYR cc_start: 0.7906 (OUTLIER) cc_final: 0.6539 (t80)
REVERT: A  315 TRP cc_start: 0.6704 (OUTLIER) cc_final: 0.5958 (t60)
REVERT: A  808 LYS cc_start: 0.7416 (OUTLIER) cc_final: 0.7143 (tttt)
REVERT: A  851 PHE cc_start: 0.5606 (OUTLIER) cc_final: 0.5335 (m-10)
REVERT: A  934 LYS cc_start: 0.7782 (OUTLIER) cc_final: 0.7402 (tttm)
REVERT: A 1062 LYS cc_start: 0.6645 (tptt) cc_final: 0.6120 (tttt)
  outliers start: 26
  outliers final: 21
  residues processed: 128
  average time/residue: 0.1830
  time to fit residues: 34.3576
Evaluate side-chains
  135 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 109
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 TYR
Chi-restraints excluded: chain A residue  132 GLN
Chi-restraints excluded: chain A residue  188 ASP
Chi-restraints excluded: chain A residue  239 PHE
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  315 TRP
Chi-restraints excluded: chain A residue  535 GLN
Chi-restraints excluded: chain A residue  808 LYS
Chi-restraints excluded: chain A residue  811 THR
Chi-restraints excluded: chain A residue  851 PHE
Chi-restraints excluded: chain A residue  911 THR
Chi-restraints excluded: chain A residue  913 GLU
Chi-restraints excluded: chain A residue  918 HIS
Chi-restraints excluded: chain A residue  934 LYS
Chi-restraints excluded: chain A residue  963 LEU
Chi-restraints excluded: chain A residue 1010 MET
Chi-restraints excluded: chain A residue 1050 ILE
Chi-restraints excluded: chain A residue 1065 THR
Chi-restraints excluded: chain A residue 1078 THR
Chi-restraints excluded: chain A residue 1083 LEU
Chi-restraints excluded: chain A residue 1121 ILE
Chi-restraints excluded: chain A residue 1140 VAL
Chi-restraints excluded: chain A residue 1190 LEU
Chi-restraints excluded: chain A residue 1213 VAL
Chi-restraints excluded: chain A residue 1230 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 60 optimal weight:    5.9990
   chunk 79 optimal weight:    3.9990
   chunk 64 optimal weight:    0.8980
   chunk 94 optimal weight:    5.9990
   chunk 47 optimal weight:    0.0670
   chunk 2 optimal weight:    0.9980
   chunk 74 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 46 optimal weight:    0.6980
   chunk 4 optimal weight:    7.9990
   chunk 68 optimal weight:    0.3980
   overall best weight:    0.5918

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

Flipped N/Q/H residues before XYZ refinement:
** A 508 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 = 0.4113 r_free = 0.4113 target = 0.182088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.157852 restraints weight = 12582.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.156333 restraints weight = 17903.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.158156 restraints weight = 16082.134|
|-----------------------------------------------------------------------------|
r_work (final): 0.3811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7536
moved from start:          0.2581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8806  Z= 0.149
  Angle     :  0.521  12.974  11816  Z= 0.276
  Chirality :  0.039   0.191   1348
  Planarity :  0.003   0.036   1465
  Dihedral  :  6.909  57.962   1364
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.92 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 20.31 %
    Favored  : 76.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.26), residues: 1081
  helix:  2.09 (0.20), residues: 694
  sheet: -0.85 (0.77), residues: 52
  loop : -1.89 (0.32), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 315 
 HIS   0.001   0.000   HIS A  61 
 PHE   0.022   0.001   PHE A 767 
 TYR   0.042   0.002   TYR A 998 
 ARG   0.002   0.000   ARG A 467 

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 111
  time to evaluate  : 0.924 
Fit side-chains
REVERT: A   75 MET cc_start: 0.6438 (ttt) cc_final: 0.5670 (mtp)
REVERT: A  117 TYR cc_start: 0.7918 (OUTLIER) cc_final: 0.6570 (t80)
REVERT: A  297 ILE cc_start: 0.8398 (tp) cc_final: 0.8149 (mt)
REVERT: A  315 TRP cc_start: 0.6732 (OUTLIER) cc_final: 0.6296 (t-100)
REVERT: A  851 PHE cc_start: 0.5623 (OUTLIER) cc_final: 0.5356 (m-10)
REVERT: A  934 LYS cc_start: 0.7778 (OUTLIER) cc_final: 0.7394 (tttm)
REVERT: A 1062 LYS cc_start: 0.6501 (tptt) cc_final: 0.6039 (tttt)
  outliers start: 28
  outliers final: 22
  residues processed: 131
  average time/residue: 0.1764
  time to fit residues: 33.8556
Evaluate side-chains
  135 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 109
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 TYR
Chi-restraints excluded: chain A residue  132 GLN
Chi-restraints excluded: chain A residue  188 ASP
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  239 PHE
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  315 TRP
Chi-restraints excluded: chain A residue  535 GLN
Chi-restraints excluded: chain A residue  808 LYS
Chi-restraints excluded: chain A residue  811 THR
Chi-restraints excluded: chain A residue  851 PHE
Chi-restraints excluded: chain A residue  911 THR
Chi-restraints excluded: chain A residue  913 GLU
Chi-restraints excluded: chain A residue  918 HIS
Chi-restraints excluded: chain A residue  934 LYS
Chi-restraints excluded: chain A residue  963 LEU
Chi-restraints excluded: chain A residue 1010 MET
Chi-restraints excluded: chain A residue 1050 ILE
Chi-restraints excluded: chain A residue 1065 THR
Chi-restraints excluded: chain A residue 1078 THR
Chi-restraints excluded: chain A residue 1083 LEU
Chi-restraints excluded: chain A residue 1121 ILE
Chi-restraints excluded: chain A residue 1140 VAL
Chi-restraints excluded: chain A residue 1213 VAL
Chi-restraints excluded: chain A residue 1230 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 104 optimal weight:    0.9990
   chunk 22 optimal weight:    0.6980
   chunk 14 optimal weight:    3.9990
   chunk 99 optimal weight:    0.9980
   chunk 24 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9980
   chunk 102 optimal weight:    6.9990
   chunk 12 optimal weight:    0.1980
   chunk 33 optimal weight:    2.9990
   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 508 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 = 0.4107 r_free = 0.4107 target = 0.181285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.153615 restraints weight = 12614.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.151031 restraints weight = 15158.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.152555 restraints weight = 16742.708|
|-----------------------------------------------------------------------------|
r_work (final): 0.3772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.2610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8806  Z= 0.160
  Angle     :  0.523  12.564  11816  Z= 0.278
  Chirality :  0.039   0.177   1348
  Planarity :  0.003   0.034   1465
  Dihedral  :  6.935  55.320   1364
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.29 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 19.87 %
    Favored  : 76.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.26), residues: 1081
  helix:  2.05 (0.19), residues: 693
  sheet: -0.10 (0.85), residues: 42
  loop : -1.99 (0.32), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 315 
 HIS   0.002   0.000   HIS A 518 
 PHE   0.024   0.001   PHE A1157 
 TYR   0.041   0.002   TYR A 998 
 ARG   0.002   0.000   ARG A 467 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2619.70 seconds
wall clock time: 47 minutes 14.95 seconds (2834.95 seconds total)