Starting phenix.real_space_refine
on Wed Sep 17 15:04:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ms8_48568/09_2025/9ms8_48568.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ms8_48568/09_2025/9ms8_48568.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.73
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ms8_48568/09_2025/9ms8_48568.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ms8_48568/09_2025/9ms8_48568.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ms8_48568/09_2025/9ms8_48568.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ms8_48568/09_2025/9ms8_48568.map"
  }
  resolution = 3.73
  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=   0.004 sd=   0.044
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      53      5.16       5
     C    6020      2.51       5
     N    1533      2.21       5
     O    1684      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  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: 9290
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 7667
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 978, 7667
          Classifications: {'peptide': 978}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 40, 'TRANS': 937}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 72
          Unresolved non-hydrogen angles: 91
          Unresolved non-hydrogen dihedrals: 54
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 4, 'GLN:plan1': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 33
    Chain: "L"
      Number of atoms: 772
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 772
          Classifications: {'peptide': 102}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 95}
    Chain: "H"
      Number of atoms: 851
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 851
          Classifications: {'peptide': 109}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 106}
  Time building chain proxies: 2.41, per 1000 atoms: 0.26
  Number of scatterers: 9290
  At special positions: 0
  Unit cell: (83.3, 108.29, 139.111, 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      53     16.00
     O    1684      8.00
     N    1533      7.00
     C    6020      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 203 " - pdb=" SG  CYS A 226 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 234 " - pdb=" SG  CYS A 327 " distance=2.02
    Simple disulfide: pdb=" SG  CYS L  42 " - pdb=" SG  CYS L 108 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  41 " - pdb=" SG  CYS H 115 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.11
  Conformation dependent library (CDL) restraints added in 435.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2362 Ramachandran restraints generated.
    1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2210

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 6 sheets defined
      53.5% alpha, 7.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 76 through 96
      removed outlier: 4.294A  pdb=" N   ARG A  80 " --> pdb=" O   PRO A  76 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LYS A  96 " --> pdb=" O   CYS A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 116
      removed outlier: 3.982A  pdb=" N   VAL A 103 " --> pdb=" O   GLY A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 124 through 129
    Processing helix  chain 'A' and resid 134 through 146
      removed outlier: 3.808A  pdb=" N   ARG A 138 " --> pdb=" O   GLY A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 187
      removed outlier: 3.511A  pdb=" N   ARG A 187 " --> pdb=" O   LEU A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 224
    Processing helix  chain 'A' and resid 230 through 235
    Processing helix  chain 'A' and resid 260 through 271
      removed outlier: 3.726A  pdb=" N   ILE A 271 " --> pdb=" O   GLU A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 285
    Processing helix  chain 'A' and resid 338 through 342
      removed outlier: 3.840A  pdb=" N   ILE A 342 " --> pdb=" O   GLN A 338 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 338 through 342'
    Processing helix  chain 'A' and resid 368 through 377
    Processing helix  chain 'A' and resid 388 through 411
      removed outlier: 3.761A  pdb=" N   ALA A 392 " --> pdb=" O   ASN A 388 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   VAL A 411 " --> pdb=" O   VAL A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 423 through 436
    Processing helix  chain 'A' and resid 438 through 457
    Processing helix  chain 'A' and resid 469 through 491
    Processing helix  chain 'A' and resid 502 through 528
      removed outlier: 3.647A  pdb=" N   LEU A 508 " --> pdb=" O   PRO A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 535 through 563
      removed outlier: 5.554A  pdb=" N   ALA A 546 " --> pdb=" O   LYS A 542 " (cutoff:3.500A)
      removed outlier: 5.582A  pdb=" N   SER A 547 " --> pdb=" O   ARG A 543 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 567 through 602
      Proline residue:  A 593  - end of helix
    Processing helix  chain 'A' and resid 733 through 746
      Proline residue:  A 742  - end of helix
      removed outlier: 4.603A  pdb=" N   LYS A 746 " --> pdb=" O   PRO A 742 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 746 through 770
      removed outlier: 3.655A  pdb=" N   LYS A 750 " --> pdb=" O   LYS A 746 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   ARG A 770 " --> pdb=" O   TYR A 766 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 776 through 780
    Processing helix  chain 'A' and resid 785 through 798
      removed outlier: 3.843A  pdb=" N   ASP A 789 " --> pdb=" O   THR A 785 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 816 through 825
    Processing helix  chain 'A' and resid 826 through 829
    Processing helix  chain 'A' and resid 843 through 866
      removed outlier: 3.751A  pdb=" N   TYR A 847 " --> pdb=" O   MET A 843 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 871 through 875
      removed outlier: 3.862A  pdb=" N   LYS A 874 " --> pdb=" O   ASN A 871 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 877 through 889
      removed outlier: 3.677A  pdb=" N   GLN A 889 " --> pdb=" O   LYS A 885 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 897 through 901
      removed outlier: 3.596A  pdb=" N   GLN A 901 " --> pdb=" O   ASP A 898 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 915 through 917
      No H-bonds generated for 'chain 'A' and resid 915 through 917'
    Processing helix  chain 'A' and resid 918 through 930
      removed outlier: 3.822A  pdb=" N   SER A 928 " --> pdb=" O   THR A 924 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 930 through 938
    Processing helix  chain 'A' and resid 956 through 960
      removed outlier: 4.178A  pdb=" N   ARG A 960 " --> pdb=" O   PRO A 957 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 985 through 1005
      removed outlier: 3.545A  pdb=" N   GLU A 989 " --> pdb=" O   SER A 985 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1012 through 1018
    Processing helix  chain 'A' and resid 1019 through 1022
    Processing helix  chain 'A' and resid 1023 through 1048
    Processing helix  chain 'A' and resid 1049 through 1075
    Processing helix  chain 'A' and resid 1079 through 1105
      removed outlier: 3.796A  pdb=" N   VAL A1090 " --> pdb=" O   LEU A1086 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   GLY A1091 " --> pdb=" O   ILE A1087 " (cutoff:3.500A)
      removed outlier: 4.250A  pdb=" N   GLU A1095 " --> pdb=" O   GLY A1091 " (cutoff:3.500A)
      removed outlier: 4.609A  pdb=" N   PHE A1096 " --> pdb=" O   ILE A1092 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   ALA A1103 " --> pdb=" O   HIS A1099 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   PHE A1104 " --> pdb=" O   VAL A1100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1112 through 1122
    Processing helix  chain 'A' and resid 1123 through 1139
      removed outlier: 3.515A  pdb=" N   LEU A1127 " --> pdb=" O   PHE A1123 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   MET A1139 " --> pdb=" O   LEU A1135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1140 through 1143
    Processing helix  chain 'A' and resid 1145 through 1170
    Processing helix  chain 'A' and resid 1170 through 1176
    Processing helix  chain 'L' and resid 49 through 51
      No H-bonds generated for 'chain 'L' and resid 49 through 51'
    Processing helix  chain 'L' and resid 99 through 103
      removed outlier: 3.650A  pdb=" N   ASP L 102 " --> pdb=" O   GLU L  99 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   ALA L 103 " --> pdb=" O   ALA L 100 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 99 through 103'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 343 through 344
    Processing sheet with id=AA2, first strand: chain 'A' and resid 800 through 807
      removed outlier: 3.531A  pdb=" N   ILE A 805 " --> pdb=" O   PHE A 974 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'L' and resid 23 through 24
      removed outlier: 3.678A  pdb=" N   SER L  90 " --> pdb=" O   SER L  87 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 65 through 69
      removed outlier: 6.477A  pdb=" N   TRP L  55 " --> pdb=" O   TRP L  67 " (cutoff:3.500A)
      removed outlier: 5.067A  pdb=" N   TYR L  69 " --> pdb=" O   LEU L  53 " (cutoff:3.500A)
      removed outlier: 7.046A  pdb=" N   LEU L  53 " --> pdb=" O   TYR L  69 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 24 through 26
      removed outlier: 3.504A  pdb=" N   LEU H 100 " --> pdb=" O   LEU H  39 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LEU H  98 " --> pdb=" O   CYS H  41 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 77 through 79
      removed outlier: 3.583A  pdb=" N   TYR H  78 " --> pdb=" O   TYR H  69 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   TYR H  69 " --> pdb=" O   TYR H  78 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   TRP H  55 " --> pdb=" O   VAL H  67 " (cutoff:3.500A)
      removed outlier: 5.095A  pdb=" N   TYR H  69 " --> pdb=" O   MET H  53 " (cutoff:3.500A)
      removed outlier: 7.226A  pdb=" N   MET H  53 " --> pdb=" O   TYR H  69 " (cutoff:3.500A)

    484 hydrogen bonds defined for protein.
    1392 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: 1.64

  Time building geometry restraints manager: 1.40 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2913
        1.34 -     1.46: 2211
        1.46 -     1.58: 4310
        1.58 -     1.70: 0
        1.70 -     1.82: 87
  Bond restraints: 9521
  Sorted by residual:
  bond pdb=" C   SER L  26 "
       pdb=" N   PRO L  27 "
    ideal  model  delta    sigma   weight residual
    1.333  1.348 -0.015 1.20e-02 6.94e+03 1.48e+00
  bond pdb=" CG  LEU L  53 "
       pdb=" CD1 LEU L  53 "
    ideal  model  delta    sigma   weight residual
    1.521  1.481  0.040 3.30e-02 9.18e+02 1.45e+00
  bond pdb=" CA  PHE A 153 "
       pdb=" CB  PHE A 153 "
    ideal  model  delta    sigma   weight residual
    1.530  1.550 -0.020 1.69e-02 3.50e+03 1.38e+00
  bond pdb=" CA  ILE A 897 "
       pdb=" CB  ILE A 897 "
    ideal  model  delta    sigma   weight residual
    1.540  1.524  0.016 1.36e-02 5.41e+03 1.35e+00
  bond pdb=" C   MET A 956 "
       pdb=" N   PRO A 957 "
    ideal  model  delta    sigma   weight residual
    1.334  1.361 -0.027 2.34e-02 1.83e+03 1.30e+00
  ... (remaining 9516 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.55: 12745
        2.55 -     5.09: 169
        5.09 -     7.64: 19
        7.64 -    10.18: 10
       10.18 -    12.73: 1
  Bond angle restraints: 12944
  Sorted by residual:
  angle pdb=" N   PRO A 896 "
        pdb=" CA  PRO A 896 "
        pdb=" CB  PRO A 896 "
      ideal   model   delta    sigma   weight residual
     103.25  110.03   -6.78 1.05e+00 9.07e-01 4.17e+01
  angle pdb=" CA  GLU A 122 "
        pdb=" CB  GLU A 122 "
        pdb=" CG  GLU A 122 "
      ideal   model   delta    sigma   weight residual
     114.10  124.00   -9.90 2.00e+00 2.50e-01 2.45e+01
  angle pdb=" CA  GLN A 839 "
        pdb=" CB  GLN A 839 "
        pdb=" CG  GLN A 839 "
      ideal   model   delta    sigma   weight residual
     114.10  123.46   -9.36 2.00e+00 2.50e-01 2.19e+01
  angle pdb=" CB  MET A 869 "
        pdb=" CG  MET A 869 "
        pdb=" SD  MET A 869 "
      ideal   model   delta    sigma   weight residual
     112.70  125.43  -12.73 3.00e+00 1.11e-01 1.80e+01
  angle pdb=" C   SER L  70 "
        pdb=" N   THR L  71 "
        pdb=" CA  THR L  71 "
      ideal   model   delta    sigma   weight residual
     121.54  129.42   -7.88 1.91e+00 2.74e-01 1.70e+01
  ... (remaining 12939 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 4845
       17.95 -    35.91: 587
       35.91 -    53.86: 136
       53.86 -    71.81: 20
       71.81 -    89.77: 9
  Dihedral angle restraints: 5597
    sinusoidal: 2146
      harmonic: 3451
  Sorted by residual:
  dihedral pdb=" CB  CYS A 203 "
           pdb=" SG  CYS A 203 "
           pdb=" SG  CYS A 226 "
           pdb=" CB  CYS A 226 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -153.08   67.08     1      1.00e+01 1.00e-02 5.86e+01
  dihedral pdb=" CA  TRP A 197 "
           pdb=" C   TRP A 197 "
           pdb=" N   LYS A 198 "
           pdb=" CA  LYS A 198 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -146.91  -33.09     0      5.00e+00 4.00e-02 4.38e+01
  dihedral pdb=" CA  CYS A 226 "
           pdb=" C   CYS A 226 "
           pdb=" N   LEU A 227 "
           pdb=" CA  LEU A 227 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.96  -20.04     0      5.00e+00 4.00e-02 1.61e+01
  ... (remaining 5594 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 1028
       0.041 -    0.082: 319
       0.082 -    0.123: 97
       0.123 -    0.164: 16
       0.164 -    0.206: 2
  Chirality restraints: 1462
  Sorted by residual:
  chirality pdb=" CA  PRO A 896 "
            pdb=" N   PRO A 896 "
            pdb=" C   PRO A 896 "
            pdb=" CB  PRO A 896 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.51    0.21 2.00e-01 2.50e+01 1.06e+00
  chirality pdb=" CB  ILE A 815 "
            pdb=" CA  ILE A 815 "
            pdb=" CG1 ILE A 815 "
            pdb=" CG2 ILE A 815 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.18 2.00e-01 2.50e+01 8.45e-01
  chirality pdb=" CG  LEU A 517 "
            pdb=" CB  LEU A 517 "
            pdb=" CD1 LEU A 517 "
            pdb=" CD2 LEU A 517 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.29e-01
  ... (remaining 1459 not shown)

  Planarity restraints: 1628
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A1149 "   -0.011 2.00e-02 2.50e+03   2.14e-02 4.58e+00
        pdb=" C   VAL A1149 "    0.037 2.00e-02 2.50e+03
        pdb=" O   VAL A1149 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   ARG A1150 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A1150 "   -0.011 2.00e-02 2.50e+03   2.14e-02 4.58e+00
        pdb=" C   ARG A1150 "    0.037 2.00e-02 2.50e+03
        pdb=" O   ARG A1150 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   TYR A1151 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 308 "    0.035 5.00e-02 4.00e+02   5.35e-02 4.57e+00
        pdb=" N   PRO A 309 "   -0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO A 309 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 309 "    0.030 5.00e-02 4.00e+02
  ... (remaining 1625 not shown)

  Histogram of nonbonded interaction distances:
        2.52 -     3.00: 5175
        3.00 -     3.47: 10019
        3.47 -     3.95: 14159
        3.95 -     4.42: 16363
        4.42 -     4.90: 26188
  Nonbonded interactions: 71904
  Sorted by model distance:
  nonbonded pdb=" O   GLU A 122 "
            pdb=" OE1 GLU A 122 "
     model   vdw
     2.522 3.040
  nonbonded pdb=" OE1 GLU H  61 "
            pdb=" N   LYS H  62 "
     model   vdw
     2.561 3.120
  nonbonded pdb=" C   SER A 928 "
            pdb=" OG  SER A 928 "
     model   vdw
     2.588 2.616
  nonbonded pdb=" N   GLY A 244 "
            pdb=" N   THR A 245 "
     model   vdw
     2.590 2.560
  nonbonded pdb=" N   ILE A 147 "
            pdb=" N   GLY A 148 "
     model   vdw
     2.595 2.560
  ... (remaining 71899 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             2.870
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     11.360
  Find NCS groups from input model:        0.050
  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:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
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   0.040   9525  Z= 0.154
  Angle     :  0.751  12.726  12952  Z= 0.382
  Chirality :  0.044   0.206   1462
  Planarity :  0.005   0.053   1628
  Dihedral  : 16.237  89.765   3375
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.04 %
    Favored  : 91.96 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 21.91 %
    Favored  : 76.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: 1181
  helix:  1.43 (0.23), residues: 548
  sheet: -1.99 (0.46), residues: 137
  loop : -2.64 (0.28), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 536 
 TYR   0.012   0.001   TYR A 766 
 PHE   0.022   0.001   PHE L  91 
 TRP   0.020   0.002   TRP H  66 
 HIS   0.006   0.001   HIS A 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 9521)
  covalent geometry    : angle       0.75041 (12944)
  SS BOND              : bond        0.00424 (    4)
  SS BOND              : angle       1.29578 (    8)
  hydrogen bonds       : bond        0.14869 (  484)
  hydrogen bonds       : angle       6.03260 ( 1392)

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

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

  2362 Ramachandran restraints generated.
    1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2362 Ramachandran restraints generated.
    1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 170
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  280 GLU cc_start: 0.9064 (tp30) cc_final: 0.8643 (tm-30)
REVERT: A  292 MET cc_start: 0.8184 (mtp) cc_final: 0.7661 (mtp)
REVERT: A  372 MET cc_start: 0.9057 (ttt) cc_final: 0.8822 (ttp)
REVERT: A  464 LYS cc_start: 0.7550 (mmtt) cc_final: 0.7217 (mmtt)
REVERT: A  598 MET cc_start: 0.8218 (tmm) cc_final: 0.7982 (mmt)
REVERT: A  748 LYS cc_start: 0.6764 (mmtm) cc_final: 0.6071 (ttpp)
REVERT: A  819 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8373 (tt)
REVERT: A 1066 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7501 (mp0)
REVERT: L   90 SER cc_start: 0.8468 (t) cc_final: 0.8087 (p)
REVERT: H   25 GLU cc_start: 0.8254 (mp0) cc_final: 0.8033 (mp0)
  outliers start: 11
  outliers final: 7
  residues processed: 177
  average time/residue: 0.0863
  time to fit residues: 22.5025
Evaluate side-chains
  155 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 147
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  508 LEU
Chi-restraints excluded: chain A residue  600 LEU
Chi-restraints excluded: chain A residue  819 LEU
Chi-restraints excluded: chain A residue 1169 VAL
Chi-restraints excluded: chain H residue   21 VAL
Chi-restraints excluded: chain H residue  108 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 108 optimal weight:    9.9990
   chunk 49 optimal weight:    0.0270
   chunk 97 optimal weight:    8.9990
   chunk 113 optimal weight:    0.4980
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    2.9990
   overall best weight:    1.0442

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

Flipped N/Q/H residues before XYZ refinement:
** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  25 GLN
L  57 GLN
** L 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 112 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.128592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.103371 restraints weight = 20105.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.106625 restraints weight = 11105.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.108849 restraints weight = 7630.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.110162 restraints weight = 6028.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.111136 restraints weight = 5215.274|
|-----------------------------------------------------------------------------|
r_work (final): 0.3560
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.0981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9525  Z= 0.147
  Angle     :  0.663   9.160  12952  Z= 0.332
  Chirality :  0.042   0.166   1462
  Planarity :  0.005   0.050   1628
  Dihedral  :  5.614  56.819   1304
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.55 %
    Favored  : 91.45 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 21.20 %
    Favored  : 74.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: 1181
  helix:  1.51 (0.22), residues: 558
  sheet: -1.70 (0.47), residues: 129
  loop : -2.58 (0.27), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  37 
 TYR   0.013   0.001   TYR A 922 
 PHE   0.024   0.002   PHE A1104 
 TRP   0.013   0.001   TRP H  66 
 HIS   0.006   0.001   HIS A 944 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 9521)
  covalent geometry    : angle       0.66249 (12944)
  SS BOND              : bond        0.00533 (    4)
  SS BOND              : angle       0.99006 (    8)
  hydrogen bonds       : bond        0.04623 (  484)
  hydrogen bonds       : angle       4.84472 ( 1392)

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

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

  2362 Ramachandran restraints generated.
    1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2362 Ramachandran restraints generated.
    1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 170
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  280 GLU cc_start: 0.8976 (tp30) cc_final: 0.8531 (tm-30)
REVERT: A  292 MET cc_start: 0.8250 (mtp) cc_final: 0.7951 (mtp)
REVERT: A  372 MET cc_start: 0.9100 (ttt) cc_final: 0.8866 (ttp)
REVERT: A  464 LYS cc_start: 0.7777 (mmtt) cc_final: 0.7395 (mmtt)
REVERT: A  598 MET cc_start: 0.8238 (tmm) cc_final: 0.7976 (mmt)
REVERT: A  734 SER cc_start: 0.8112 (m) cc_final: 0.7811 (t)
REVERT: A  748 LYS cc_start: 0.6533 (mmtm) cc_final: 0.5915 (ttpp)
REVERT: A  819 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8502 (tt)
REVERT: A  956 MET cc_start: 0.8669 (tmm) cc_final: 0.8420 (tmm)
REVERT: A 1066 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7471 (mp0)
REVERT: L   90 SER cc_start: 0.8613 (t) cc_final: 0.8018 (p)
REVERT: L   99 GLU cc_start: 0.7369 (mp0) cc_final: 0.6978 (mp0)
REVERT: H   62 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7576 (mtpt)
  outliers start: 41
  outliers final: 26
  residues processed: 196
  average time/residue: 0.0808
  time to fit residues: 23.8315
Evaluate side-chains
  177 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 149
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  220 ILE
Chi-restraints excluded: chain A residue  335 MET
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  388 ASN
Chi-restraints excluded: chain A residue  508 LEU
Chi-restraints excluded: chain A residue  525 THR
Chi-restraints excluded: chain A residue  540 CYS
Chi-restraints excluded: chain A residue  560 PHE
Chi-restraints excluded: chain A residue  582 VAL
Chi-restraints excluded: chain A residue  583 PHE
Chi-restraints excluded: chain A residue  600 LEU
Chi-restraints excluded: chain A residue  773 ASP
Chi-restraints excluded: chain A residue  819 LEU
Chi-restraints excluded: chain A residue 1131 VAL
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1139 MET
Chi-restraints excluded: chain A residue 1169 VAL
Chi-restraints excluded: chain A residue 1171 LEU
Chi-restraints excluded: chain L residue   92 SER
Chi-restraints excluded: chain H residue   21 VAL
Chi-restraints excluded: chain H residue   26 SER
Chi-restraints excluded: chain H residue   62 LYS
Chi-restraints excluded: chain H residue  103 THR
Chi-restraints excluded: chain H residue  121 MET
Chi-restraints excluded: chain H residue  126 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 60 optimal weight:    0.8980
   chunk 99 optimal weight:   10.0000
   chunk 72 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   chunk 111 optimal weight:    4.9990
   chunk 103 optimal weight:    3.9990
   chunk 66 optimal weight:    8.9990
   chunk 28 optimal weight:    2.9990
   chunk 109 optimal weight:    6.9990
   chunk 65 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9980
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1121 HIS
** L 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 112 HIS
H  58 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.128308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.103983 restraints weight = 20214.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.107260 restraints weight = 10920.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.109477 restraints weight = 7423.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.110857 restraints weight = 5807.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.111742 restraints weight = 4974.987|
|-----------------------------------------------------------------------------|
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.1340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9525  Z= 0.143
  Angle     :  0.650  10.467  12952  Z= 0.321
  Chirality :  0.042   0.198   1462
  Planarity :  0.004   0.051   1628
  Dihedral  :  5.306  55.790   1299
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.87 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 22.92 %
    Favored  : 72.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.59 (0.26), residues: 1181
  helix:  1.56 (0.22), residues: 559
  sheet: -1.62 (0.44), residues: 139
  loop : -2.48 (0.28), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H 117 
 TYR   0.021   0.001   TYR A 766 
 PHE   0.018   0.001   PHE A1104 
 TRP   0.010   0.001   TRP H  66 
 HIS   0.006   0.001   HIS A1099 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 9521)
  covalent geometry    : angle       0.64949 (12944)
  SS BOND              : bond        0.00495 (    4)
  SS BOND              : angle       0.89538 (    8)
  hydrogen bonds       : bond        0.04305 (  484)
  hydrogen bonds       : angle       4.61711 ( 1392)

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

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

  2362 Ramachandran restraints generated.
    1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2362 Ramachandran restraints generated.
    1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 155
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  202 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7386 (pt)
REVERT: A  280 GLU cc_start: 0.8969 (tp30) cc_final: 0.8580 (tm-30)
REVERT: A  292 MET cc_start: 0.8254 (mtp) cc_final: 0.7906 (mtp)
REVERT: A  464 LYS cc_start: 0.7738 (mmtt) cc_final: 0.7374 (mmtt)
REVERT: A  598 MET cc_start: 0.8250 (tmm) cc_final: 0.7986 (mmt)
REVERT: A  734 SER cc_start: 0.8112 (m) cc_final: 0.7826 (t)
REVERT: A  748 LYS cc_start: 0.6579 (mmtm) cc_final: 0.5835 (ttpp)
REVERT: A  956 MET cc_start: 0.8650 (tmm) cc_final: 0.8416 (tmm)
REVERT: A 1066 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7494 (mp0)
REVERT: A 1165 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8167 (tp)
REVERT: H   62 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7613 (mtpt)
  outliers start: 47
  outliers final: 30
  residues processed: 185
  average time/residue: 0.0818
  time to fit residues: 22.4516
Evaluate side-chains
  179 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 146
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  388 ASN
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  508 LEU
Chi-restraints excluded: chain A residue  525 THR
Chi-restraints excluded: chain A residue  540 CYS
Chi-restraints excluded: chain A residue  560 PHE
Chi-restraints excluded: chain A residue  582 VAL
Chi-restraints excluded: chain A residue  583 PHE
Chi-restraints excluded: chain A residue  773 ASP
Chi-restraints excluded: chain A residue  835 GLU
Chi-restraints excluded: chain A residue  969 ILE
Chi-restraints excluded: chain A residue 1131 VAL
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1165 LEU
Chi-restraints excluded: chain A residue 1169 VAL
Chi-restraints excluded: chain L residue   29 ILE
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain L residue   41 THR
Chi-restraints excluded: chain H residue   21 VAL
Chi-restraints excluded: chain H residue   49 SER
Chi-restraints excluded: chain H residue   62 LYS
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain H residue  103 THR
Chi-restraints excluded: chain H residue  108 GLU
Chi-restraints excluded: chain H residue  121 MET
Chi-restraints excluded: chain H residue  126 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 96 optimal weight:    0.7980
   chunk 116 optimal weight:    0.9990
   chunk 112 optimal weight:    0.7980
   chunk 82 optimal weight:    1.9990
   chunk 17 optimal weight:    0.2980
   chunk 84 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9980
   chunk 114 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 58 optimal weight:    6.9990
   chunk 49 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 808 GLN
** L 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 112 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.135412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.110518 restraints weight = 20061.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.113917 restraints weight = 10856.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.116289 restraints weight = 7414.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.117807 restraints weight = 5797.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.118516 restraints weight = 4939.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.1635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9525  Z= 0.125
  Angle     :  0.638  10.004  12952  Z= 0.313
  Chirality :  0.041   0.208   1462
  Planarity :  0.004   0.049   1628
  Dihedral  :  4.903  45.161   1295
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.13 %
    Favored  : 91.87 %
  Rotamer:
    Outliers :  5.48 %
    Allowed  : 23.33 %
    Favored  : 71.20 %
  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: -0.43 (0.26), residues: 1181
  helix:  1.65 (0.22), residues: 561
  sheet: -1.57 (0.44), residues: 139
  loop : -2.34 (0.29), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  37 
 TYR   0.020   0.001   TYR A 766 
 PHE   0.017   0.001   PHE L  76 
 TRP   0.011   0.001   TRP A 197 
 HIS   0.006   0.001   HIS A1099 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 9521)
  covalent geometry    : angle       0.63812 (12944)
  SS BOND              : bond        0.00485 (    4)
  SS BOND              : angle       0.75825 (    8)
  hydrogen bonds       : bond        0.03948 (  484)
  hydrogen bonds       : angle       4.49225 ( 1392)

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

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

  2362 Ramachandran restraints generated.
    1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2362 Ramachandran restraints generated.
    1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 164
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  280 GLU cc_start: 0.8925 (tp30) cc_final: 0.8603 (tm-30)
REVERT: A  464 LYS cc_start: 0.7718 (mmtt) cc_final: 0.7384 (mmtt)
REVERT: A  598 MET cc_start: 0.8295 (tmm) cc_final: 0.8015 (mmt)
REVERT: A  734 SER cc_start: 0.8062 (m) cc_final: 0.7761 (t)
REVERT: A  748 LYS cc_start: 0.6572 (mmtm) cc_final: 0.5800 (ttpp)
REVERT: A 1066 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7543 (mp0)
REVERT: L   99 GLU cc_start: 0.7762 (mp0) cc_final: 0.7433 (mp0)
REVERT: H   62 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7567 (mtpt)
REVERT: H   66 TRP cc_start: 0.8367 (t60) cc_final: 0.7898 (t60)
  outliers start: 54
  outliers final: 41
  residues processed: 197
  average time/residue: 0.0798
  time to fit residues: 23.1920
Evaluate side-chains
  192 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 150
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 PHE
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  220 ILE
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  335 MET
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  388 ASN
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  508 LEU
Chi-restraints excluded: chain A residue  525 THR
Chi-restraints excluded: chain A residue  540 CYS
Chi-restraints excluded: chain A residue  551 THR
Chi-restraints excluded: chain A residue  560 PHE
Chi-restraints excluded: chain A residue  582 VAL
Chi-restraints excluded: chain A residue  583 PHE
Chi-restraints excluded: chain A residue  744 LEU
Chi-restraints excluded: chain A residue  773 ASP
Chi-restraints excluded: chain A residue  835 GLU
Chi-restraints excluded: chain A residue  937 SER
Chi-restraints excluded: chain A residue  969 ILE
Chi-restraints excluded: chain A residue 1062 LEU
Chi-restraints excluded: chain A residue 1131 VAL
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1169 VAL
Chi-restraints excluded: chain A residue 1170 LEU
Chi-restraints excluded: chain L residue   29 ILE
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain L residue   41 THR
Chi-restraints excluded: chain L residue   92 SER
Chi-restraints excluded: chain L residue   95 ILE
Chi-restraints excluded: chain H residue   21 VAL
Chi-restraints excluded: chain H residue   31 VAL
Chi-restraints excluded: chain H residue   62 LYS
Chi-restraints excluded: chain H residue   77 ILE
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain H residue  103 THR
Chi-restraints excluded: chain H residue  108 GLU
Chi-restraints excluded: chain H residue  121 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 46 optimal weight:    0.8980
   chunk 111 optimal weight:    2.9990
   chunk 94 optimal weight:    0.0970
   chunk 19 optimal weight:    3.9990
   chunk 82 optimal weight:    0.0010
   chunk 88 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9990
   chunk 99 optimal weight:    9.9990
   chunk 76 optimal weight:    5.9990
   chunk 14 optimal weight:    0.8980
   chunk 57 optimal weight:    3.9990
   overall best weight:    0.5786

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

Flipped N/Q/H residues before XYZ refinement:
** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  57 GLN
L  58 GLN
** L 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 112 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.136315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.111073 restraints weight = 19982.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.114487 restraints weight = 10834.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.116784 restraints weight = 7451.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.118301 restraints weight = 5863.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.119294 restraints weight = 5013.665|
|-----------------------------------------------------------------------------|
r_work (final): 0.3661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.1962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9525  Z= 0.120
  Angle     :  0.644  10.700  12952  Z= 0.313
  Chirality :  0.041   0.142   1462
  Planarity :  0.004   0.048   1628
  Dihedral  :  4.765  29.842   1295
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.37 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  6.19 %
    Allowed  : 23.94 %
    Favored  : 69.88 %
  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: -0.34 (0.26), residues: 1181
  helix:  1.70 (0.22), residues: 560
  sheet: -1.60 (0.44), residues: 144
  loop : -2.21 (0.29), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  86 
 TYR   0.015   0.001   TYR A 820 
 PHE   0.019   0.001   PHE L  76 
 TRP   0.009   0.001   TRP A 197 
 HIS   0.004   0.001   HIS L 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 9521)
  covalent geometry    : angle       0.64394 (12944)
  SS BOND              : bond        0.00444 (    4)
  SS BOND              : angle       0.68723 (    8)
  hydrogen bonds       : bond        0.03735 (  484)
  hydrogen bonds       : angle       4.43091 ( 1392)

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

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

  2362 Ramachandran restraints generated.
    1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2362 Ramachandran restraints generated.
    1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 169
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  280 GLU cc_start: 0.8928 (tp30) cc_final: 0.8606 (tm-30)
REVERT: A  292 MET cc_start: 0.8258 (mtp) cc_final: 0.7739 (mtp)
REVERT: A  598 MET cc_start: 0.8291 (tmm) cc_final: 0.8001 (mmt)
REVERT: A  734 SER cc_start: 0.7985 (m) cc_final: 0.7703 (t)
REVERT: A  748 LYS cc_start: 0.6550 (mmtm) cc_final: 0.5786 (ttpp)
REVERT: A  974 PHE cc_start: 0.8963 (OUTLIER) cc_final: 0.8615 (p90)
REVERT: A 1051 TRP cc_start: 0.7767 (OUTLIER) cc_final: 0.6048 (t60)
REVERT: A 1066 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7554 (mp0)
REVERT: L   56 TYR cc_start: 0.8805 (m-80) cc_final: 0.8555 (m-80)
REVERT: L   99 GLU cc_start: 0.7798 (mp0) cc_final: 0.7463 (mp0)
REVERT: H   22 GLN cc_start: 0.7446 (mp10) cc_final: 0.7230 (mp10)
REVERT: H   62 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7520 (mtpt)
REVERT: H   66 TRP cc_start: 0.8368 (t60) cc_final: 0.7801 (t60)
REVERT: H  126 GLN cc_start: 0.8031 (mm110) cc_final: 0.7770 (mm110)
  outliers start: 61
  outliers final: 38
  residues processed: 210
  average time/residue: 0.0814
  time to fit residues: 25.3389
Evaluate side-chains
  202 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 161
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 PHE
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  220 ILE
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  367 MET
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  525 THR
Chi-restraints excluded: chain A residue  540 CYS
Chi-restraints excluded: chain A residue  551 THR
Chi-restraints excluded: chain A residue  560 PHE
Chi-restraints excluded: chain A residue  582 VAL
Chi-restraints excluded: chain A residue  583 PHE
Chi-restraints excluded: chain A residue  773 ASP
Chi-restraints excluded: chain A residue  835 GLU
Chi-restraints excluded: chain A residue  862 ASP
Chi-restraints excluded: chain A residue  937 SER
Chi-restraints excluded: chain A residue  969 ILE
Chi-restraints excluded: chain A residue  974 PHE
Chi-restraints excluded: chain A residue 1051 TRP
Chi-restraints excluded: chain A residue 1062 LEU
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1169 VAL
Chi-restraints excluded: chain L residue   29 ILE
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain L residue   41 THR
Chi-restraints excluded: chain L residue   95 ILE
Chi-restraints excluded: chain H residue   21 VAL
Chi-restraints excluded: chain H residue   31 VAL
Chi-restraints excluded: chain H residue   49 SER
Chi-restraints excluded: chain H residue   62 LYS
Chi-restraints excluded: chain H residue   77 ILE
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain H residue  103 THR
Chi-restraints excluded: chain H residue  108 GLU
Chi-restraints excluded: chain H residue  121 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 58 optimal weight:    0.6980
   chunk 64 optimal weight:    5.9990
   chunk 4 optimal weight:    2.9990
   chunk 70 optimal weight:   10.0000
   chunk 55 optimal weight:    4.9990
   chunk 34 optimal weight:    4.9990
   chunk 108 optimal weight:    1.9990
   chunk 99 optimal weight:    0.7980
   chunk 88 optimal weight:    0.1980
   chunk 43 optimal weight:    0.7980
   chunk 44 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 156 GLN
** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  57 GLN
** L 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 112 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.137047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.112134 restraints weight = 20053.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.115638 restraints weight = 10782.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.117944 restraints weight = 7303.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.119312 restraints weight = 5734.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.120299 restraints weight = 4934.371|
|-----------------------------------------------------------------------------|
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.2192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9525  Z= 0.120
  Angle     :  0.646  10.965  12952  Z= 0.313
  Chirality :  0.041   0.160   1462
  Planarity :  0.004   0.047   1628
  Dihedral  :  4.589  24.356   1293
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.37 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  4.97 %
    Allowed  : 26.06 %
    Favored  : 68.97 %
  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: -0.22 (0.26), residues: 1181
  helix:  1.73 (0.22), residues: 563
  sheet: -1.45 (0.45), residues: 140
  loop : -2.13 (0.29), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 144 
 TYR   0.015   0.001   TYR A 820 
 PHE   0.019   0.001   PHE A 798 
 TRP   0.021   0.001   TRP A  78 
 HIS   0.005   0.001   HIS A1099 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 9521)
  covalent geometry    : angle       0.64587 (12944)
  SS BOND              : bond        0.00456 (    4)
  SS BOND              : angle       0.65081 (    8)
  hydrogen bonds       : bond        0.03682 (  484)
  hydrogen bonds       : angle       4.41752 ( 1392)

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

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

  2362 Ramachandran restraints generated.
    1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2362 Ramachandran restraints generated.
    1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 161
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  280 GLU cc_start: 0.8932 (tp30) cc_final: 0.8618 (tm-30)
REVERT: A  292 MET cc_start: 0.8276 (mtp) cc_final: 0.7709 (mtp)
REVERT: A  464 LYS cc_start: 0.7759 (mptt) cc_final: 0.7518 (mmtt)
REVERT: A  598 MET cc_start: 0.8436 (tmm) cc_final: 0.8036 (mmt)
REVERT: A  734 SER cc_start: 0.7992 (m) cc_final: 0.7693 (t)
REVERT: A  974 PHE cc_start: 0.8982 (OUTLIER) cc_final: 0.8608 (p90)
REVERT: A 1051 TRP cc_start: 0.7730 (OUTLIER) cc_final: 0.6061 (t60)
REVERT: A 1066 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7603 (mp0)
REVERT: A 1166 ASN cc_start: 0.8387 (m-40) cc_final: 0.8130 (t0)
REVERT: L   99 GLU cc_start: 0.7876 (mp0) cc_final: 0.7626 (mp0)
REVERT: H   62 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7489 (mtpt)
REVERT: H   66 TRP cc_start: 0.8409 (t60) cc_final: 0.7915 (t60)
REVERT: H  126 GLN cc_start: 0.8038 (mm110) cc_final: 0.7787 (mm110)
  outliers start: 49
  outliers final: 36
  residues processed: 192
  average time/residue: 0.0878
  time to fit residues: 24.5757
Evaluate side-chains
  190 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 151
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  367 MET
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  525 THR
Chi-restraints excluded: chain A residue  540 CYS
Chi-restraints excluded: chain A residue  551 THR
Chi-restraints excluded: chain A residue  560 PHE
Chi-restraints excluded: chain A residue  582 VAL
Chi-restraints excluded: chain A residue  583 PHE
Chi-restraints excluded: chain A residue  773 ASP
Chi-restraints excluded: chain A residue  835 GLU
Chi-restraints excluded: chain A residue  862 ASP
Chi-restraints excluded: chain A residue  937 SER
Chi-restraints excluded: chain A residue  969 ILE
Chi-restraints excluded: chain A residue  974 PHE
Chi-restraints excluded: chain A residue 1051 TRP
Chi-restraints excluded: chain A residue 1062 LEU
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1169 VAL
Chi-restraints excluded: chain A residue 1170 LEU
Chi-restraints excluded: chain L residue   29 ILE
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain L residue   53 LEU
Chi-restraints excluded: chain L residue   95 ILE
Chi-restraints excluded: chain H residue   21 VAL
Chi-restraints excluded: chain H residue   31 VAL
Chi-restraints excluded: chain H residue   62 LYS
Chi-restraints excluded: chain H residue   77 ILE
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain H residue  108 GLU
Chi-restraints excluded: chain H residue  121 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 88 optimal weight:    0.0060
   chunk 42 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9980
   chunk 61 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 66 optimal weight:   10.0000
   chunk 59 optimal weight:    0.9990
   chunk 96 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   overall best weight:    0.7196

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

Flipped N/Q/H residues before XYZ refinement:
** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  57 GLN
** L 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 112 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.137362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.112294 restraints weight = 20033.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.115834 restraints weight = 10806.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.118126 restraints weight = 7357.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.119694 restraints weight = 5766.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.120555 restraints weight = 4913.272|
|-----------------------------------------------------------------------------|
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.2364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9525  Z= 0.119
  Angle     :  0.631  10.388  12952  Z= 0.308
  Chirality :  0.041   0.161   1462
  Planarity :  0.004   0.047   1628
  Dihedral  :  4.540  24.944   1293
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.62 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  5.98 %
    Allowed  : 25.25 %
    Favored  : 68.76 %
  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: -0.18 (0.26), residues: 1181
  helix:  1.75 (0.22), residues: 564
  sheet: -1.42 (0.44), residues: 140
  loop : -2.10 (0.29), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L 113 
 TYR   0.022   0.001   TYR H 114 
 PHE   0.021   0.001   PHE L  76 
 TRP   0.019   0.001   TRP A  78 
 HIS   0.004   0.001   HIS H  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 9521)
  covalent geometry    : angle       0.63053 (12944)
  SS BOND              : bond        0.00454 (    4)
  SS BOND              : angle       0.67798 (    8)
  hydrogen bonds       : bond        0.03625 (  484)
  hydrogen bonds       : angle       4.33959 ( 1392)

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

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

  2362 Ramachandran restraints generated.
    1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2362 Ramachandran restraints generated.
    1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 162
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  280 GLU cc_start: 0.8894 (tp30) cc_final: 0.8643 (tm-30)
REVERT: A  292 MET cc_start: 0.8249 (mtp) cc_final: 0.7711 (mtp)
REVERT: A  598 MET cc_start: 0.8418 (tmm) cc_final: 0.7989 (mmt)
REVERT: A  734 SER cc_start: 0.7988 (m) cc_final: 0.7691 (t)
REVERT: A  974 PHE cc_start: 0.8992 (OUTLIER) cc_final: 0.8613 (p90)
REVERT: A 1051 TRP cc_start: 0.7734 (OUTLIER) cc_final: 0.6076 (t60)
REVERT: A 1066 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7581 (mp0)
REVERT: A 1166 ASN cc_start: 0.8376 (m-40) cc_final: 0.8096 (t0)
REVERT: L   99 GLU cc_start: 0.7927 (mp0) cc_final: 0.7715 (mp0)
REVERT: H   62 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7477 (mtpt)
REVERT: H   66 TRP cc_start: 0.8432 (t60) cc_final: 0.7917 (t60)
REVERT: H  126 GLN cc_start: 0.8075 (mm110) cc_final: 0.7827 (mm110)
  outliers start: 59
  outliers final: 38
  residues processed: 201
  average time/residue: 0.0819
  time to fit residues: 24.4516
Evaluate side-chains
  196 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 155
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  220 ILE
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  365 GLN
Chi-restraints excluded: chain A residue  415 SER
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  525 THR
Chi-restraints excluded: chain A residue  540 CYS
Chi-restraints excluded: chain A residue  551 THR
Chi-restraints excluded: chain A residue  560 PHE
Chi-restraints excluded: chain A residue  582 VAL
Chi-restraints excluded: chain A residue  583 PHE
Chi-restraints excluded: chain A residue  737 GLU
Chi-restraints excluded: chain A residue  773 ASP
Chi-restraints excluded: chain A residue  835 GLU
Chi-restraints excluded: chain A residue  937 SER
Chi-restraints excluded: chain A residue  969 ILE
Chi-restraints excluded: chain A residue  974 PHE
Chi-restraints excluded: chain A residue 1051 TRP
Chi-restraints excluded: chain A residue 1062 LEU
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1169 VAL
Chi-restraints excluded: chain A residue 1170 LEU
Chi-restraints excluded: chain L residue   29 ILE
Chi-restraints excluded: chain L residue   40 LEU
Chi-restraints excluded: chain L residue   41 THR
Chi-restraints excluded: chain L residue   95 ILE
Chi-restraints excluded: chain H residue   21 VAL
Chi-restraints excluded: chain H residue   31 VAL
Chi-restraints excluded: chain H residue   49 SER
Chi-restraints excluded: chain H residue   62 LYS
Chi-restraints excluded: chain H residue   77 ILE
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain H residue  108 GLU
Chi-restraints excluded: chain H residue  121 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 109 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 71 optimal weight:    9.9990
   chunk 68 optimal weight:    0.4980
   chunk 87 optimal weight:    3.9990
   chunk 9 optimal weight:    5.9990
   chunk 112 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 60 optimal weight:    0.7980
   chunk 83 optimal weight:    0.9990
   overall best weight:    0.8586

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

Flipped N/Q/H residues before XYZ refinement:
** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 944 HIS
L  58 GLN
** L 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 112 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.132647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.109749 restraints weight = 19247.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.113131 restraints weight = 10061.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.115391 restraints weight = 6719.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.116871 restraints weight = 5175.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.117585 restraints weight = 4350.637|
|-----------------------------------------------------------------------------|
r_work (final): 0.3683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.2480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9525  Z= 0.126
  Angle     :  0.657  12.990  12952  Z= 0.317
  Chirality :  0.041   0.258   1462
  Planarity :  0.004   0.045   1628
  Dihedral  :  4.538  24.651   1293
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.79 %
    Favored  : 92.21 %
  Rotamer:
    Outliers :  5.58 %
    Allowed  : 25.66 %
    Favored  : 68.76 %
  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: -0.11 (0.26), residues: 1181
  helix:  1.82 (0.22), residues: 564
  sheet: -1.40 (0.44), residues: 138
  loop : -2.06 (0.29), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H 117 
 TYR   0.022   0.001   TYR H 114 
 PHE   0.022   0.001   PHE L  76 
 TRP   0.019   0.001   TRP A  78 
 HIS   0.004   0.001   HIS H  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 9521)
  covalent geometry    : angle       0.65682 (12944)
  SS BOND              : bond        0.00482 (    4)
  SS BOND              : angle       0.74593 (    8)
  hydrogen bonds       : bond        0.03599 (  484)
  hydrogen bonds       : angle       4.34093 ( 1392)

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

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

  2362 Ramachandran restraints generated.
    1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2362 Ramachandran restraints generated.
    1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 156
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 TYR cc_start: 0.7051 (m-80) cc_final: 0.6767 (m-80)
REVERT: A  292 MET cc_start: 0.8243 (mtp) cc_final: 0.7715 (mtp)
REVERT: A  598 MET cc_start: 0.8416 (tmm) cc_final: 0.7994 (mmt)
REVERT: A  974 PHE cc_start: 0.8997 (OUTLIER) cc_final: 0.8245 (p90)
REVERT: A 1051 TRP cc_start: 0.7708 (OUTLIER) cc_final: 0.6064 (t60)
REVERT: A 1066 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7580 (mp0)
REVERT: H   62 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7463 (mtpt)
REVERT: H   66 TRP cc_start: 0.8473 (t60) cc_final: 0.7909 (t60)
REVERT: H  126 GLN cc_start: 0.8101 (mm110) cc_final: 0.7825 (mm110)
  outliers start: 55
  outliers final: 42
  residues processed: 192
  average time/residue: 0.0798
  time to fit residues: 22.8355
Evaluate side-chains
  195 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 150
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  220 ILE
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  365 GLN
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  444 SER
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  525 THR
Chi-restraints excluded: chain A residue  540 CYS
Chi-restraints excluded: chain A residue  551 THR
Chi-restraints excluded: chain A residue  560 PHE
Chi-restraints excluded: chain A residue  582 VAL
Chi-restraints excluded: chain A residue  583 PHE
Chi-restraints excluded: chain A residue  737 GLU
Chi-restraints excluded: chain A residue  773 ASP
Chi-restraints excluded: chain A residue  835 GLU
Chi-restraints excluded: chain A residue  862 ASP
Chi-restraints excluded: chain A residue  932 VAL
Chi-restraints excluded: chain A residue  937 SER
Chi-restraints excluded: chain A residue  969 ILE
Chi-restraints excluded: chain A residue  974 PHE
Chi-restraints excluded: chain A residue 1051 TRP
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1169 VAL
Chi-restraints excluded: chain A residue 1170 LEU
Chi-restraints excluded: chain L residue   29 ILE
Chi-restraints excluded: chain L residue   40 LEU
Chi-restraints excluded: chain L residue   41 THR
Chi-restraints excluded: chain L residue   95 ILE
Chi-restraints excluded: chain H residue   21 VAL
Chi-restraints excluded: chain H residue   26 SER
Chi-restraints excluded: chain H residue   49 SER
Chi-restraints excluded: chain H residue   62 LYS
Chi-restraints excluded: chain H residue   77 ILE
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain H residue  108 GLU
Chi-restraints excluded: chain H residue  121 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 28 optimal weight:    3.9990
   chunk 45 optimal weight:    5.9990
   chunk 69 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0010
   chunk 43 optimal weight:    0.8980
   chunk 68 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 91 optimal weight:    5.9990
   overall best weight:    0.7586

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

Flipped N/Q/H residues before XYZ refinement:
** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  58 GLN
** L 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 112 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.136388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.111332 restraints weight = 19801.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.114797 restraints weight = 10733.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.117113 restraints weight = 7365.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.118453 restraints weight = 5799.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.119513 restraints weight = 5019.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.2604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9525  Z= 0.125
  Angle     :  0.671  12.870  12952  Z= 0.323
  Chirality :  0.041   0.228   1462
  Planarity :  0.004   0.046   1628
  Dihedral  :  4.551  24.642   1293
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.71 %
    Favored  : 92.29 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 26.67 %
    Favored  : 68.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.11 (0.26), residues: 1181
  helix:  1.78 (0.22), residues: 565
  sheet: -1.43 (0.44), residues: 138
  loop : -2.02 (0.29), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  37 
 TYR   0.011   0.001   TYR A 820 
 PHE   0.022   0.001   PHE L  91 
 TRP   0.020   0.001   TRP A  78 
 HIS   0.004   0.001   HIS A1099 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 9521)
  covalent geometry    : angle       0.67075 (12944)
  SS BOND              : bond        0.00469 (    4)
  SS BOND              : angle       0.73662 (    8)
  hydrogen bonds       : bond        0.03599 (  484)
  hydrogen bonds       : angle       4.31519 ( 1392)

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

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

  2362 Ramachandran restraints generated.
    1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2362 Ramachandran restraints generated.
    1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 154
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 TYR cc_start: 0.7145 (m-80) cc_final: 0.6845 (m-80)
REVERT: A  292 MET cc_start: 0.8265 (mtp) cc_final: 0.7720 (mtp)
REVERT: A  464 LYS cc_start: 0.7905 (mmtt) cc_final: 0.7492 (pttm)
REVERT: A  598 MET cc_start: 0.8413 (tmm) cc_final: 0.7961 (mmt)
REVERT: A  869 MET cc_start: 0.7518 (mmm) cc_final: 0.6739 (mmm)
REVERT: A  974 PHE cc_start: 0.8993 (OUTLIER) cc_final: 0.8247 (p90)
REVERT: A 1051 TRP cc_start: 0.7724 (OUTLIER) cc_final: 0.6042 (t60)
REVERT: A 1066 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7670 (mp0)
REVERT: L   99 GLU cc_start: 0.7460 (mp0) cc_final: 0.6946 (mp0)
REVERT: H   62 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7476 (mtpt)
REVERT: H   66 TRP cc_start: 0.8471 (t60) cc_final: 0.7939 (t60)
REVERT: H  126 GLN cc_start: 0.8154 (mm110) cc_final: 0.7787 (mm110)
  outliers start: 48
  outliers final: 38
  residues processed: 188
  average time/residue: 0.0808
  time to fit residues: 22.6882
Evaluate side-chains
  189 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 148
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  220 ILE
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  365 GLN
Chi-restraints excluded: chain A residue  415 SER
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  525 THR
Chi-restraints excluded: chain A residue  540 CYS
Chi-restraints excluded: chain A residue  551 THR
Chi-restraints excluded: chain A residue  560 PHE
Chi-restraints excluded: chain A residue  582 VAL
Chi-restraints excluded: chain A residue  583 PHE
Chi-restraints excluded: chain A residue  773 ASP
Chi-restraints excluded: chain A residue  835 GLU
Chi-restraints excluded: chain A residue  932 VAL
Chi-restraints excluded: chain A residue  937 SER
Chi-restraints excluded: chain A residue  969 ILE
Chi-restraints excluded: chain A residue  974 PHE
Chi-restraints excluded: chain A residue 1051 TRP
Chi-restraints excluded: chain A residue 1131 VAL
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1169 VAL
Chi-restraints excluded: chain A residue 1170 LEU
Chi-restraints excluded: chain L residue   40 LEU
Chi-restraints excluded: chain L residue   41 THR
Chi-restraints excluded: chain L residue   95 ILE
Chi-restraints excluded: chain H residue   21 VAL
Chi-restraints excluded: chain H residue   49 SER
Chi-restraints excluded: chain H residue   62 LYS
Chi-restraints excluded: chain H residue   77 ILE
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain H residue  108 GLU
Chi-restraints excluded: chain H residue  121 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 59 optimal weight:    4.9990
   chunk 9 optimal weight:   10.0000
   chunk 87 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 109 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 89 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 70 optimal weight:    9.9990
   chunk 114 optimal weight:    4.9990
   chunk 12 optimal weight:    0.5980
   overall best weight:    1.8786

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

Flipped N/Q/H residues before XYZ refinement:
** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  58 GLN
** L 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 112 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.127901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.102195 restraints weight = 20086.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.105503 restraints weight = 11189.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.107673 restraints weight = 7772.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.109060 restraints weight = 6180.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.109745 restraints weight = 5348.863|
|-----------------------------------------------------------------------------|
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.2618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9525  Z= 0.192
  Angle     :  0.718  13.201  12952  Z= 0.351
  Chirality :  0.043   0.210   1462
  Planarity :  0.005   0.044   1628
  Dihedral  :  4.853  27.254   1293
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.04 %
    Favored  : 91.96 %
  Rotamer:
    Outliers :  4.97 %
    Allowed  : 26.98 %
    Favored  : 68.05 %
  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: -0.12 (0.26), residues: 1181
  helix:  1.81 (0.22), residues: 560
  sheet: -1.58 (0.43), residues: 139
  loop : -1.98 (0.29), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L 113 
 TYR   0.022   0.001   TYR H 114 
 PHE   0.023   0.002   PHE L  76 
 TRP   0.022   0.001   TRP A  78 
 HIS   0.005   0.001   HIS A 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 ( 9521)
  covalent geometry    : angle       0.71456 (12944)
  SS BOND              : bond        0.00824 (    4)
  SS BOND              : angle       2.86847 (    8)
  hydrogen bonds       : bond        0.04092 (  484)
  hydrogen bonds       : angle       4.42083 ( 1392)

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

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

  2362 Ramachandran restraints generated.
    1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2362 Ramachandran restraints generated.
    1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 149
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 TYR cc_start: 0.7265 (m-80) cc_final: 0.6905 (m-80)
REVERT: A  292 MET cc_start: 0.8287 (mtp) cc_final: 0.7679 (mtp)
REVERT: A  464 LYS cc_start: 0.7956 (mmtt) cc_final: 0.7473 (pttm)
REVERT: A  598 MET cc_start: 0.8432 (tmm) cc_final: 0.7975 (mmt)
REVERT: A  869 MET cc_start: 0.7692 (mmm) cc_final: 0.6877 (mmm)
REVERT: A 1051 TRP cc_start: 0.7771 (OUTLIER) cc_final: 0.6124 (t60)
REVERT: A 1066 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7557 (mp0)
REVERT: L   99 GLU cc_start: 0.7466 (mp0) cc_final: 0.6940 (mp0)
REVERT: H   25 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8060 (mp0)
REVERT: H   53 MET cc_start: 0.8199 (mmt) cc_final: 0.7844 (mmt)
REVERT: H   62 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7515 (mtpt)
REVERT: H   66 TRP cc_start: 0.8636 (t60) cc_final: 0.8112 (t60)
  outliers start: 49
  outliers final: 41
  residues processed: 184
  average time/residue: 0.0751
  time to fit residues: 20.7669
Evaluate side-chains
  188 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 144
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  220 ILE
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  365 GLN
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  444 SER
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  525 THR
Chi-restraints excluded: chain A residue  540 CYS
Chi-restraints excluded: chain A residue  551 THR
Chi-restraints excluded: chain A residue  560 PHE
Chi-restraints excluded: chain A residue  582 VAL
Chi-restraints excluded: chain A residue  583 PHE
Chi-restraints excluded: chain A residue  737 GLU
Chi-restraints excluded: chain A residue  773 ASP
Chi-restraints excluded: chain A residue  862 ASP
Chi-restraints excluded: chain A residue  932 VAL
Chi-restraints excluded: chain A residue  937 SER
Chi-restraints excluded: chain A residue  969 ILE
Chi-restraints excluded: chain A residue  974 PHE
Chi-restraints excluded: chain A residue 1051 TRP
Chi-restraints excluded: chain A residue 1131 VAL
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1159 LEU
Chi-restraints excluded: chain A residue 1169 VAL
Chi-restraints excluded: chain A residue 1170 LEU
Chi-restraints excluded: chain L residue   40 LEU
Chi-restraints excluded: chain L residue   41 THR
Chi-restraints excluded: chain L residue   95 ILE
Chi-restraints excluded: chain H residue   21 VAL
Chi-restraints excluded: chain H residue   25 GLU
Chi-restraints excluded: chain H residue   31 VAL
Chi-restraints excluded: chain H residue   49 SER
Chi-restraints excluded: chain H residue   62 LYS
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain H residue  108 GLU
Chi-restraints excluded: chain H residue  121 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 91 optimal weight:    0.5980
   chunk 69 optimal weight:    3.9990
   chunk 3 optimal weight:    4.9990
   chunk 79 optimal weight:    2.9990
   chunk 51 optimal weight:    0.7980
   chunk 47 optimal weight:    0.8980
   chunk 57 optimal weight:    3.9990
   chunk 19 optimal weight:    0.1980
   chunk 31 optimal weight:    0.9980
   chunk 95 optimal weight:    0.6980
   chunk 56 optimal weight:    5.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  58 GLN
** L 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.134509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.111439 restraints weight = 19041.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.114764 restraints weight = 10151.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.117006 restraints weight = 6749.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.118370 restraints weight = 5214.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.119302 restraints weight = 4438.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.3678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.2746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9525  Z= 0.125
  Angle     :  0.684  13.043  12952  Z= 0.329
  Chirality :  0.041   0.207   1462
  Planarity :  0.004   0.046   1628
  Dihedral  :  4.714  27.974   1293
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.45 %
    Favored  : 92.55 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 27.79 %
    Favored  : 68.26 %
  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: -0.06 (0.26), residues: 1181
  helix:  1.84 (0.22), residues: 560
  sheet: -1.52 (0.44), residues: 139
  loop : -1.93 (0.30), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H 117 
 TYR   0.010   0.001   TYR H 114 
 PHE   0.025   0.001   PHE L  76 
 TRP   0.025   0.001   TRP A  78 
 HIS   0.004   0.001   HIS H  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 9521)
  covalent geometry    : angle       0.68232 (12944)
  SS BOND              : bond        0.00466 (    4)
  SS BOND              : angle       2.14678 (    8)
  hydrogen bonds       : bond        0.03676 (  484)
  hydrogen bonds       : angle       4.32288 ( 1392)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1748.77 seconds
wall clock time: 30 minutes 59.31 seconds (1859.31 seconds total)