Starting phenix.real_space_refine
on Wed Sep 17 12:36:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cr8_45854/09_2025/9cr8_45854.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cr8_45854/09_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_45854/09_2025/9cr8_45854.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cr8_45854/09_2025/9cr8_45854.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cr8_45854/09_2025/9cr8_45854.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cr8_45854/09_2025/9cr8_45854.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.23, per 1000 atoms: 0.26
  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: 0.84
  Conformation dependent library (CDL) restraints added in 323.5 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  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: 0.31
  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: 1.46

  Time building geometry restraints manager: 1.05 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:             1.420
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.800
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  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:1.190
  Set ADP refinement strategy:             0.010
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.660
-------------------------------------------------------------------------------
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= 0.156
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.002   0.000   ARG A 699 
 TYR   0.021   0.001   TYR A 247 
 PHE   0.011   0.001   PHE A  72 
 TRP   0.009   0.001   TRP A 698 
 HIS   0.002   0.001   HIS A1007 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 8806)
  covalent geometry    : angle       0.49402 (11816)
  hydrogen bonds       : bond        0.16187 (  521)
  hydrogen bonds       : angle       5.54363 ( 1539)

*********************** 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  : 0.356 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 MET cc_start: 0.6481 (ttt) cc_final: 0.5568 (mtp)
REVERT: A  380 LYS cc_start: 0.7684 (ptpp) cc_final: 0.6618 (ttpt)
REVERT: A  450 MET cc_start: 0.7276 (ptp) cc_final: 0.6915 (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: 0.7949 (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: 0.7170 (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: 0.6091 (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: 0.0971
  time to fit residues: 22.6686
Evaluate side-chains
  124 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 123
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
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 49 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9990
   chunk 53 optimal weight:   20.0000
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    7.9990
   chunk 100 optimal weight:    4.9990
   chunk 106 optimal weight:   10.0000
   chunk 38 optimal weight:    4.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 487 ASN
A 535 GLN
A 587 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.174678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.149275 restraints weight = 12787.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.147372 restraints weight = 17338.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.148647 restraints weight = 16764.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.148488 restraints weight = 12125.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.148940 restraints weight = 12236.252|
|-----------------------------------------------------------------------------|
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.1420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8806  Z= 0.187
  Angle     :  0.571   6.528  11816  Z= 0.310
  Chirality :  0.041   0.149   1348
  Planarity :  0.004   0.040   1465
  Dihedral  :  7.998  61.369   1364
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 13.92 %
    Favored  : 82.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.66 (0.26), residues: 1081
  helix:  1.66 (0.20), residues: 681
  sheet: -1.26 (0.72), residues: 62
  loop : -1.82 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 467 
 TYR   0.040   0.002   TYR A 998 
 PHE   0.020   0.001   PHE A  72 
 TRP   0.010   0.002   TRP A 803 
 HIS   0.003   0.001   HIS A 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 8806)
  covalent geometry    : angle       0.57105 (11816)
  hydrogen bonds       : bond        0.06018 (  521)
  hydrogen bonds       : angle       4.34272 ( 1539)

*********************** 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
  157 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 127
  time to evaluate  : 0.317 
Fit side-chains
REVERT: A  502 LYS cc_start: 0.7765 (mtpp) cc_final: 0.7477 (ttmm)
REVERT: A  925 GLN cc_start: 0.7932 (tm-30) cc_final: 0.7355 (tt0)
REVERT: A  934 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7544 (tttm)
REVERT: A  951 PHE cc_start: 0.7010 (t80) cc_final: 0.6742 (t80)
REVERT: A 1061 LYS cc_start: 0.7794 (mtmm) cc_final: 0.6793 (ttpp)
REVERT: A 1062 LYS cc_start: 0.6808 (tptt) cc_final: 0.6076 (tttt)
  outliers start: 30
  outliers final: 21
  residues processed: 146
  average time/residue: 0.0908
  time to fit residues: 18.8777
Evaluate side-chains
  136 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 114
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
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  263 THR
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  700 ILE
Chi-restraints excluded: chain A residue  811 THR
Chi-restraints excluded: chain A residue  898 THR
Chi-restraints excluded: chain A residue  911 THR
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 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
Chi-restraints excluded: chain A residue 1190 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 69 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9990
   chunk 27 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   chunk 37 optimal weight:   20.0000
   chunk 11 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 83 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** A 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 750 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.177154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.153935 restraints weight = 12653.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.151946 restraints weight = 20221.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.150243 restraints weight = 17976.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.150250 restraints weight = 14726.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.150677 restraints weight = 12674.381|
|-----------------------------------------------------------------------------|
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.1750

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= 0.129
  Angle     :  0.503   6.540  11816  Z= 0.274
  Chirality :  0.039   0.151   1348
  Planarity :  0.003   0.043   1465
  Dihedral  :  7.622  56.366   1364
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.29 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 15.26 %
    Favored  : 81.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.85 (0.26), residues: 1081
  helix:  1.85 (0.20), residues: 684
  sheet: -1.30 (0.72), residues: 62
  loop : -1.86 (0.32), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1147 
 TYR   0.034   0.002   TYR A 998 
 PHE   0.012   0.001   PHE A 601 
 TRP   0.009   0.001   TRP A 315 
 HIS   0.002   0.001   HIS A 398 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 8806)
  covalent geometry    : angle       0.50312 (11816)
  hydrogen bonds       : bond        0.05239 (  521)
  hydrogen bonds       : angle       4.02995 ( 1539)

*********************** 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
  151 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 125
  time to evaluate  : 0.315 
Fit side-chains
REVERT: A  192 MET cc_start: 0.8209 (tpp) cc_final: 0.7902 (tpp)
REVERT: A  925 GLN cc_start: 0.7839 (tm-30) cc_final: 0.7266 (tt0)
REVERT: A  934 LYS cc_start: 0.7818 (OUTLIER) cc_final: 0.7490 (tttm)
REVERT: A 1062 LYS cc_start: 0.6818 (tptt) cc_final: 0.6168 (tttt)
  outliers start: 26
  outliers final: 20
  residues processed: 141
  average time/residue: 0.0811
  time to fit residues: 16.6025
Evaluate side-chains
  131 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 110
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
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  305 LEU
Chi-restraints excluded: chain A residue  460 THR
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  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  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 1121 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 37 optimal weight:   20.0000
   chunk 47 optimal weight:    3.9990
   chunk 44 optimal weight:    6.9990
   chunk 102 optimal weight:    0.7980
   chunk 106 optimal weight:    9.9990
   chunk 71 optimal weight:    3.9990
   chunk 31 optimal weight:    0.0670
   chunk 6 optimal weight:    0.8980
   chunk 97 optimal weight:    6.9990
   chunk 53 optimal weight:   10.0000
   chunk 107 optimal weight:    6.9990
   overall best weight:    1.9522

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

Flipped N/Q/H residues before XYZ refinement:
A1175 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.174705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.147392 restraints weight = 12573.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.145399 restraints weight = 16839.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.147360 restraints weight = 15164.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.147303 restraints weight = 10185.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.147639 restraints weight = 11038.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.2197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   8806  Z= 0.196
  Angle     :  0.582   7.184  11816  Z= 0.315
  Chirality :  0.041   0.146   1348
  Planarity :  0.004   0.047   1465
  Dihedral  :  8.386  59.747   1364
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 15.71 %
    Favored  : 79.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.54 (0.26), residues: 1081
  helix:  1.56 (0.19), residues: 686
  sheet: -0.93 (0.79), residues: 52
  loop : -1.97 (0.32), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1147 
 TYR   0.037   0.002   TYR A 247 
 PHE   0.015   0.002   PHE A 200 
 TRP   0.014   0.002   TRP A 315 
 HIS   0.004   0.001   HIS A 518 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 ( 8806)
  covalent geometry    : angle       0.58150 (11816)
  hydrogen bonds       : bond        0.06061 (  521)
  hydrogen bonds       : angle       4.25317 ( 1539)

*********************** 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: 39
    poor density    : 112
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
REVERT: A  192 MET cc_start: 0.8435 (tpp) cc_final: 0.8203 (tpp)
REVERT: A  736 ILE cc_start: 0.8513 (tp) cc_final: 0.8308 (tp)
REVERT: A  851 PHE cc_start: 0.6269 (OUTLIER) cc_final: 0.5942 (m-10)
REVERT: A  925 GLN cc_start: 0.7916 (tm-30) cc_final: 0.7470 (tt0)
REVERT: A  934 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7717 (tttm)
REVERT: A 1061 LYS cc_start: 0.7790 (mtmm) cc_final: 0.6823 (ttpp)
REVERT: A 1062 LYS cc_start: 0.6825 (tptt) cc_final: 0.6049 (tttt)
  outliers start: 39
  outliers final: 26
  residues processed: 139
  average time/residue: 0.0876
  time to fit residues: 17.5189
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  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 MET
Chi-restraints excluded: chain A residue  117 TYR
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  460 THR
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain A residue  535 GLN
Chi-restraints excluded: chain A residue  719 ILE
Chi-restraints excluded: chain A residue  756 SER
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  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 1065 THR
Chi-restraints excluded: chain A residue 1078 THR
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 62 optimal weight:    0.6980
   chunk 80 optimal weight:    4.9990
   chunk 107 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9980
   chunk 35 optimal weight:    0.0050
   chunk 74 optimal weight:    5.9990
   chunk 47 optimal weight:    7.9990
   chunk 36 optimal weight:    7.9990
   chunk 81 optimal weight:    0.9990
   chunk 37 optimal weight:   10.0000
   chunk 69 optimal weight:    0.9980
   overall best weight:    0.7396

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

Flipped N/Q/H residues before XYZ refinement:
A1175 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.178579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.154191 restraints weight = 12700.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.152374 restraints weight = 17827.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.152608 restraints weight = 17953.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.151690 restraints weight = 15276.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.152195 restraints weight = 12608.388|
|-----------------------------------------------------------------------------|
r_work (final): 0.3776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.2232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   8806  Z= 0.120
  Angle     :  0.500   8.102  11816  Z= 0.269
  Chirality :  0.038   0.145   1348
  Planarity :  0.003   0.046   1465
  Dihedral  :  7.747  57.528   1364
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 17.96 %
    Favored  : 78.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.88 (0.26), residues: 1081
  helix:  1.90 (0.20), residues: 685
  sheet: -1.26 (0.72), residues: 62
  loop : -1.91 (0.32), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1147 
 TYR   0.026   0.002   TYR A 998 
 PHE   0.015   0.001   PHE A 601 
 TRP   0.009   0.001   TRP A 315 
 HIS   0.002   0.000   HIS A 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 8806)
  covalent geometry    : angle       0.50047 (11816)
  hydrogen bonds       : bond        0.04962 (  521)
  hydrogen bonds       : angle       3.91665 ( 1539)

*********************** 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
  151 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 117
  time to evaluate  : 0.380 
Fit side-chains
REVERT: A  192 MET cc_start: 0.8285 (tpp) cc_final: 0.8034 (tpp)
REVERT: A  851 PHE cc_start: 0.5738 (OUTLIER) cc_final: 0.5519 (m-10)
REVERT: A  925 GLN cc_start: 0.7755 (tm-30) cc_final: 0.7246 (tt0)
REVERT: A  934 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7545 (tttm)
REVERT: A  986 MET cc_start: 0.7517 (mtp) cc_final: 0.7218 (mtm)
REVERT: A 1061 LYS cc_start: 0.7700 (mtmm) cc_final: 0.6772 (ttpp)
REVERT: A 1062 LYS cc_start: 0.6724 (tptt) cc_final: 0.5931 (tttt)
  outliers start: 34
  outliers final: 21
  residues processed: 141
  average time/residue: 0.0855
  time to fit residues: 17.4448
Evaluate side-chains
  134 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 111
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  117 TYR
Chi-restraints excluded: chain A residue  239 PHE
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  700 ILE
Chi-restraints excluded: chain A residue  756 SER
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  971 PHE
Chi-restraints excluded: chain A residue 1010 MET
Chi-restraints excluded: chain A residue 1050 ILE
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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 103 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 83 optimal weight:    0.8980
   chunk 92 optimal weight:    0.0980
   chunk 48 optimal weight:   10.0000
   chunk 43 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9980
   chunk 85 optimal weight:    6.9990
   chunk 101 optimal weight:    3.9990
   chunk 71 optimal weight:    0.8980
   overall best weight:    0.9782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.178001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 78)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.150488 restraints weight = 12642.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.148161 restraints weight = 15053.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.149347 restraints weight = 15254.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.149498 restraints weight = 13571.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.150535 restraints weight = 11238.828|
|-----------------------------------------------------------------------------|
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7639
moved from start:          0.2334

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= 0.132
  Angle     :  0.514   9.473  11816  Z= 0.277
  Chirality :  0.039   0.146   1348
  Planarity :  0.003   0.047   1465
  Dihedral  :  7.651  58.360   1364
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 18.41 %
    Favored  : 77.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.91 (0.26), residues: 1081
  helix:  1.91 (0.20), residues: 685
  sheet: -1.29 (0.69), residues: 62
  loop : -1.88 (0.32), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1147 
 TYR   0.028   0.002   TYR A 247 
 PHE   0.016   0.001   PHE A 601 
 TRP   0.008   0.001   TRP A 315 
 HIS   0.002   0.001   HIS A1155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 8806)
  covalent geometry    : angle       0.51413 (11816)
  hydrogen bonds       : bond        0.05043 (  521)
  hydrogen bonds       : angle       3.92452 ( 1539)

*********************** 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
  153 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 116
  time to evaluate  : 0.313 
Fit side-chains
REVERT: A  192 MET cc_start: 0.8344 (tpp) cc_final: 0.8081 (tpp)
REVERT: A  736 ILE cc_start: 0.8271 (tp) cc_final: 0.7880 (tp)
REVERT: A  851 PHE cc_start: 0.5847 (OUTLIER) cc_final: 0.5581 (m-10)
REVERT: A  925 GLN cc_start: 0.7822 (tm-30) cc_final: 0.7298 (tt0)
REVERT: A  934 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7580 (tttm)
REVERT: A  986 MET cc_start: 0.7545 (mtp) cc_final: 0.7334 (mtm)
REVERT: A 1061 LYS cc_start: 0.7703 (mtmm) cc_final: 0.6716 (ttpp)
REVERT: A 1062 LYS cc_start: 0.6726 (tptt) cc_final: 0.5845 (tttt)
  outliers start: 37
  outliers final: 27
  residues processed: 144
  average time/residue: 0.0841
  time to fit residues: 17.5971
Evaluate side-chains
  140 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 111
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  117 TYR
Chi-restraints excluded: chain A residue  144 ILE
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  700 ILE
Chi-restraints excluded: chain A residue  756 SER
Chi-restraints excluded: chain A residue  805 ASP
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 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 68 optimal weight:    0.6980
   chunk 80 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9980
   chunk 81 optimal weight:    0.7980
   chunk 107 optimal weight:    1.9990
   chunk 16 optimal weight:    0.3980
   chunk 23 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 76 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 96 optimal weight:    6.9990
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.180125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.153203 restraints weight = 12536.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.152337 restraints weight = 17789.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.155004 restraints weight = 15182.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.154286 restraints weight = 10988.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.155041 restraints weight = 10930.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.3801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7546
moved from start:          0.2428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8806  Z= 0.118
  Angle     :  0.500  10.340  11816  Z= 0.269
  Chirality :  0.038   0.156   1348
  Planarity :  0.003   0.046   1465
  Dihedral  :  7.403  59.964   1364
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.29 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 18.07 %
    Favored  : 78.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.03 (0.26), residues: 1081
  helix:  2.01 (0.20), residues: 685
  sheet: -1.22 (0.69), residues: 62
  loop : -1.84 (0.32), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 467 
 TYR   0.025   0.002   TYR A 247 
 PHE   0.015   0.001   PHE A 601 
 TRP   0.007   0.001   TRP A 315 
 HIS   0.001   0.000   HIS A 518 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 8806)
  covalent geometry    : angle       0.49982 (11816)
  hydrogen bonds       : bond        0.04731 (  521)
  hydrogen bonds       : angle       3.80395 ( 1539)

*********************** 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
  155 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 120
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
REVERT: A  192 MET cc_start: 0.8207 (tpp) cc_final: 0.7944 (tpp)
REVERT: A  315 TRP cc_start: 0.6898 (OUTLIER) cc_final: 0.6105 (t60)
REVERT: A  736 ILE cc_start: 0.8330 (tp) cc_final: 0.8011 (tp)
REVERT: A  738 VAL cc_start: 0.7786 (OUTLIER) cc_final: 0.7575 (t)
REVERT: A  851 PHE cc_start: 0.5768 (OUTLIER) cc_final: 0.5512 (m-10)
REVERT: A  925 GLN cc_start: 0.7713 (tm-30) cc_final: 0.7134 (tt0)
REVERT: A  934 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7483 (tttm)
REVERT: A  986 MET cc_start: 0.7517 (mtp) cc_final: 0.7266 (mtm)
REVERT: A 1061 LYS cc_start: 0.7710 (mtmm) cc_final: 0.6737 (ttpp)
REVERT: A 1062 LYS cc_start: 0.6665 (tptt) cc_final: 0.5891 (tttt)
  outliers start: 35
  outliers final: 25
  residues processed: 146
  average time/residue: 0.0822
  time to fit residues: 17.1448
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  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  117 TYR
Chi-restraints excluded: chain A residue  239 PHE
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  582 THR
Chi-restraints excluded: chain A residue  700 ILE
Chi-restraints excluded: chain A residue  738 VAL
Chi-restraints excluded: chain A residue  805 ASP
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  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 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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 85 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 54 optimal weight:   20.0000
   chunk 103 optimal weight:    4.9990
   chunk 43 optimal weight:    4.9990
   chunk 95 optimal weight:    6.9990
   chunk 18 optimal weight:    6.9990
   chunk 93 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0040
   chunk 91 optimal weight:    8.9990
   overall best weight:    2.2000

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

Flipped N/Q/H residues before XYZ refinement:
A 530 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.174410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.145931 restraints weight = 12468.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.144305 restraints weight = 15655.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.145505 restraints weight = 15281.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.146648 restraints weight = 11030.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.147008 restraints weight = 9442.540|
|-----------------------------------------------------------------------------|
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.2613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   8806  Z= 0.211
  Angle     :  0.600  11.024  11816  Z= 0.322
  Chirality :  0.042   0.160   1348
  Planarity :  0.004   0.045   1465
  Dihedral  :  8.216  56.694   1364
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.48 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 17.62 %
    Favored  : 78.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.60 (0.26), residues: 1081
  helix:  1.60 (0.19), residues: 686
  sheet: -1.31 (0.68), residues: 62
  loop : -1.86 (0.33), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 580 
 TYR   0.036   0.002   TYR A 247 
 PHE   0.016   0.002   PHE A  72 
 TRP   0.008   0.002   TRP A 315 
 HIS   0.005   0.001   HIS A 518 

Details of bonding type rmsd
  covalent geometry    : bond        0.00493 ( 8806)
  covalent geometry    : angle       0.59997 (11816)
  hydrogen bonds       : bond        0.05951 (  521)
  hydrogen bonds       : angle       4.15306 ( 1539)

*********************** 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
  149 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 111
  time to evaluate  : 0.309 
Fit side-chains
REVERT: A  192 MET cc_start: 0.8506 (tpp) cc_final: 0.8283 (tpp)
REVERT: A  736 ILE cc_start: 0.8510 (tp) cc_final: 0.8230 (tp)
REVERT: A  851 PHE cc_start: 0.6190 (OUTLIER) cc_final: 0.5888 (m-10)
REVERT: A  925 GLN cc_start: 0.7901 (tm-30) cc_final: 0.7416 (tt0)
REVERT: A  934 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7661 (tttm)
REVERT: A 1061 LYS cc_start: 0.7732 (mtmm) cc_final: 0.6782 (ttpp)
REVERT: A 1062 LYS cc_start: 0.6841 (tptt) cc_final: 0.6048 (tttt)
  outliers start: 38
  outliers final: 33
  residues processed: 137
  average time/residue: 0.0802
  time to fit residues: 16.1074
Evaluate side-chains
  145 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 110
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  117 TYR
Chi-restraints excluded: chain A residue  144 ILE
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  460 THR
Chi-restraints excluded: chain A residue  490 TYR
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain A residue  535 GLN
Chi-restraints excluded: chain A residue  700 ILE
Chi-restraints excluded: chain A residue  738 VAL
Chi-restraints excluded: chain A residue  756 SER
Chi-restraints excluded: chain A residue  805 ASP
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  963 LEU
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 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 9 optimal weight:    0.8980
   chunk 102 optimal weight:    3.9990
   chunk 34 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9980
   chunk 61 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 46 optimal weight:    4.9990
   chunk 69 optimal weight:    0.7980
   chunk 76 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9980
   chunk 84 optimal weight:    0.6980
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.178580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.151269 restraints weight = 12396.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.150097 restraints weight = 14057.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.151077 restraints weight = 15244.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.152142 restraints weight = 11103.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.152492 restraints weight = 9477.946|
|-----------------------------------------------------------------------------|
r_work (final): 0.3761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7581
moved from start:          0.2616

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= 0.125
  Angle     :  0.519  10.254  11816  Z= 0.281
  Chirality :  0.039   0.212   1348
  Planarity :  0.003   0.049   1465
  Dihedral  :  7.703  55.468   1364
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 19.19 %
    Favored  : 77.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.85 (0.26), residues: 1081
  helix:  1.85 (0.20), residues: 686
  sheet: -1.21 (0.68), residues: 62
  loop : -1.89 (0.32), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 467 
 TYR   0.025   0.002   TYR A 247 
 PHE   0.027   0.001   PHE A 601 
 TRP   0.008   0.001   TRP A 315 
 HIS   0.002   0.000   HIS A 518 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 8806)
  covalent geometry    : angle       0.51880 (11816)
  hydrogen bonds       : bond        0.05030 (  521)
  hydrogen bonds       : angle       3.87899 ( 1539)

*********************** 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
  148 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 119
  time to evaluate  : 0.329 
Fit side-chains
REVERT: A   75 MET cc_start: 0.6398 (ttt) cc_final: 0.5680 (mtp)
REVERT: A  192 MET cc_start: 0.8209 (tpp) cc_final: 0.7927 (tpp)
REVERT: A  736 ILE cc_start: 0.8427 (tp) cc_final: 0.8146 (tp)
REVERT: A  738 VAL cc_start: 0.7863 (OUTLIER) cc_final: 0.7631 (t)
REVERT: A  851 PHE cc_start: 0.5820 (OUTLIER) cc_final: 0.5556 (m-10)
REVERT: A  925 GLN cc_start: 0.7802 (tm-30) cc_final: 0.7287 (tt0)
REVERT: A  934 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7530 (tttm)
REVERT: A  986 MET cc_start: 0.7406 (mtp) cc_final: 0.7095 (mtm)
REVERT: A 1061 LYS cc_start: 0.7627 (mtmm) cc_final: 0.6647 (ttpp)
REVERT: A 1062 LYS cc_start: 0.6670 (tptt) cc_final: 0.5788 (tttt)
REVERT: A 1158 ILE cc_start: 0.7521 (tt) cc_final: 0.7301 (mt)
  outliers start: 29
  outliers final: 26
  residues processed: 137
  average time/residue: 0.0786
  time to fit residues: 15.9814
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  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  117 TYR
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  239 PHE
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  700 ILE
Chi-restraints excluded: chain A residue  738 VAL
Chi-restraints excluded: chain A residue  805 ASP
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 18 optimal weight:    6.9990
   chunk 25 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9990
   chunk 93 optimal weight:    7.9990
   chunk 41 optimal weight:    0.6980
   chunk 91 optimal weight:    6.9990
   chunk 89 optimal weight:    7.9990
   chunk 50 optimal weight:    9.9990
   chunk 100 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   overall best weight:    1.4986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.175841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.153385 restraints weight = 12737.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.152240 restraints weight = 18996.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.149923 restraints weight = 17450.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.149882 restraints weight = 17159.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.150122 restraints weight = 13016.548|
|-----------------------------------------------------------------------------|
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.2705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8806  Z= 0.165
  Angle     :  0.572  12.652  11816  Z= 0.306
  Chirality :  0.041   0.256   1348
  Planarity :  0.004   0.046   1465
  Dihedral  :  7.924  55.868   1364
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.29 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 19.53 %
    Favored  : 76.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.71 (0.26), residues: 1081
  helix:  1.69 (0.19), residues: 687
  sheet: -1.17 (0.68), residues: 62
  loop : -1.87 (0.33), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 467 
 TYR   0.032   0.002   TYR A 247 
 PHE   0.027   0.002   PHE A 601 
 TRP   0.007   0.001   TRP A 162 
 HIS   0.003   0.001   HIS A 518 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 8806)
  covalent geometry    : angle       0.57230 (11816)
  hydrogen bonds       : bond        0.05514 (  521)
  hydrogen bonds       : angle       4.01387 ( 1539)

********************** 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
  147 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 115
  time to evaluate  : 0.330 
Fit side-chains
REVERT: A   75 MET cc_start: 0.6398 (ttt) cc_final: 0.5739 (mtp)
REVERT: A  192 MET cc_start: 0.8398 (tpp) cc_final: 0.8127 (tpp)
REVERT: A  736 ILE cc_start: 0.8479 (tp) cc_final: 0.8227 (tp)
REVERT: A  851 PHE cc_start: 0.5919 (OUTLIER) cc_final: 0.5601 (m-10)
REVERT: A  925 GLN cc_start: 0.7837 (tm-30) cc_final: 0.7334 (tt0)
REVERT: A  934 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7617 (tttm)
REVERT: A 1061 LYS cc_start: 0.7602 (mtmm) cc_final: 0.6704 (ttpp)
REVERT: A 1062 LYS cc_start: 0.6725 (tptt) cc_final: 0.6032 (tttt)
  outliers start: 32
  outliers final: 28
  residues processed: 136
  average time/residue: 0.0819
  time to fit residues: 16.3267
Evaluate side-chains
  144 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 114
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  117 TYR
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  490 TYR
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain A residue  535 GLN
Chi-restraints excluded: chain A residue  700 ILE
Chi-restraints excluded: chain A residue  805 ASP
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 107 optimal weight:    2.9990
   chunk 69 optimal weight:    0.7980
   chunk 36 optimal weight:    0.0770
   chunk 23 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 21 optimal weight:    0.8980
   chunk 4 optimal weight:    5.9990
   chunk 94 optimal weight:    0.7980
   chunk 56 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 74 optimal weight:    0.0670
   overall best weight:    0.4876

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.179803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.152438 restraints weight = 12339.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.152448 restraints weight = 15966.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.153909 restraints weight = 14827.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.153779 restraints weight = 9408.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.154168 restraints weight = 9563.676|
|-----------------------------------------------------------------------------|
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.2733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8806  Z= 0.115
  Angle     :  0.524  12.350  11816  Z= 0.277
  Chirality :  0.039   0.243   1348
  Planarity :  0.003   0.049   1465
  Dihedral  :  7.292  55.825   1364
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.38 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 20.20 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.93 (0.26), residues: 1081
  helix:  1.90 (0.20), residues: 693
  sheet: -1.10 (0.68), residues: 62
  loop : -1.96 (0.32), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 580 
 TYR   0.023   0.001   TYR A 247 
 PHE   0.025   0.001   PHE A 601 
 TRP   0.006   0.001   TRP A 212 
 HIS   0.001   0.000   HIS A 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 8806)
  covalent geometry    : angle       0.52362 (11816)
  hydrogen bonds       : bond        0.04624 (  521)
  hydrogen bonds       : angle       3.76178 ( 1539)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1332.71 seconds
wall clock time: 23 minutes 51.99 seconds (1431.99 seconds total)