Starting phenix.real_space_refine
on Thu Sep 18 14:09:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kwc_62607/09_2025/9kwc_62607_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kwc_62607/09_2025/9kwc_62607.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kwc_62607/09_2025/9kwc_62607.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kwc_62607/09_2025/9kwc_62607.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kwc_62607/09_2025/9kwc_62607_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kwc_62607/09_2025/9kwc_62607_neut.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.009
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 9014 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     P      25      5.49       5
     S      24      5.16       5
     C    6074      2.51       5
     N    1579      2.21       5
     O    1912      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 86 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: 9614
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9079
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1121, 9067
          Classifications: {'peptide': 1121}
          Incomplete info: {'truncation_to_alanine': 45}
          Link IDs: {'PTRANS': 22, 'TRANS': 1098}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 175
          Unresolved non-hydrogen angles: 190
          Unresolved non-hydrogen dihedrals: 160
          Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 4, 'GLN:plan1': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 55
      Conformer: "B"
        Number of residues, atoms: 1121, 9067
          Classifications: {'peptide': 1121}
          Incomplete info: {'truncation_to_alanine': 45}
          Link IDs: {'PTRANS': 22, 'TRANS': 1098}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 175
          Unresolved non-hydrogen angles: 190
          Unresolved non-hydrogen dihedrals: 160
          Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 4, 'GLN:plan1': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 55
          bond proxies already assigned to first conformer: 9236
    Chain: "G"
      Number of atoms: 535
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 535
          Classifications: {'RNA': 25}
          Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 4, 'rna3p_pur': 7, 'rna3p_pyr': 7}
          Link IDs: {'rna2p': 10, 'rna3p': 14}
  Time building chain proxies: 3.43, per 1000 atoms: 0.36
  Number of scatterers: 9614
  At special positions: 0
  Unit cell: (81.51, 108.87, 122.55, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      24     16.00
     P      25     15.00
     O    1912      8.00
     N    1579      7.00
     C    6074      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.81
  Conformation dependent library (CDL) restraints added in 512.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2146

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 8 sheets defined
      45.5% alpha, 8.5% beta
      6 base pairs and 13 stacking pairs defined.
    Time for finding SS restraints: 1.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 7
      removed outlier: 3.846A  pdb=" N   LYS A   6 " --> pdb=" O   SER A   2 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   PHE A   7 " --> pdb=" O   LYS A   3 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 2 through 7'
    Processing helix  chain 'A' and resid 26 through 34
    Processing helix  chain 'A' and resid 37 through 69
      removed outlier: 5.633A  pdb=" N   LYS A  48 " --> pdb=" O   ALA A  44 " (cutoff:3.500A)
      removed outlier: 5.144A  pdb=" N   GLY A  49 " --> pdb=" O   GLU A  45 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   LEU A  66 " --> pdb=" O   ILE A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 109
      removed outlier: 4.364A  pdb=" N   LEU A  97 " --> pdb=" O   GLU A  93 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   LYS A 103 " --> pdb=" O   ILE A  99 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   ALA A 108 " --> pdb=" O   GLU A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 119
    Processing helix  chain 'A' and resid 121 through 126
      removed outlier: 3.728A  pdb=" N   GLU A 125 " --> pdb=" O   LYS A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 132
    Processing helix  chain 'A' and resid 134 through 144
    Processing helix  chain 'A' and resid 151 through 161
    Processing helix  chain 'A' and resid 172 through 177
    Processing helix  chain 'A' and resid 190 through 196
      removed outlier: 3.550A  pdb=" N   ALA A 195 " --> pdb=" O   LYS A 192 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   ILE A 196 " --> pdb=" O   VAL A 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 209
    Processing helix  chain 'A' and resid 210 through 214
    Processing helix  chain 'A' and resid 233 through 238
      removed outlier: 4.095A  pdb=" N   TYR A 237 " --> pdb=" O   GLY A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 260
      removed outlier: 3.547A  pdb=" N   ILE A 259 " --> pdb=" O   LEU A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 323
      removed outlier: 3.773A  pdb=" N   SER A 312 " --> pdb=" O   LEU A 308 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   SER A 316 " --> pdb=" O   SER A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 333
      removed outlier: 3.914A  pdb=" N   GLU A 330 " --> pdb=" O   LYS A 326 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   SER A 333 " --> pdb=" O   ASP A 329 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 341 through 352
      removed outlier: 4.096A  pdb=" N   SER A 345 " --> pdb=" O   GLY A 341 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   THR A 346 " --> pdb=" O   PRO A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 371
    Processing helix  chain 'A' and resid 378 through 392
      removed outlier: 3.559A  pdb=" N   GLU A 382 " --> pdb=" O   THR A 378 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 403
    Processing helix  chain 'A' and resid 409 through 430
      removed outlier: 3.535A  pdb=" N   VAL A 422 " --> pdb=" O   ILE A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 432 through 437
    Processing helix  chain 'A' and resid 449 through 472
      removed outlier: 4.388A  pdb=" N   ALA A 472 " --> pdb=" O   ASN A 468 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 497
      removed outlier: 3.623A  pdb=" N   ILE A 496 " --> pdb=" O   LEU A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 512
      removed outlier: 4.308A  pdb=" N   HIS A 502 " --> pdb=" O   LEU A 498 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ILE A 503 " --> pdb=" O   LYS A 499 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 559 through 563
      removed outlier: 3.719A  pdb=" N   ALA A 563 " --> pdb=" O   LYS A 560 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 564 through 569
      removed outlier: 3.630A  pdb=" N   LYS A 568 " --> pdb=" O   LYS A 564 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 687 through 697
    Processing helix  chain 'A' and resid 706 through 710
      removed outlier: 3.520A  pdb=" N   SER A 710 " --> pdb=" O   LYS A 707 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 718 through 728
      removed outlier: 3.608A  pdb=" N   PHE A 728 " --> pdb=" O   PHE A 724 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 752 through 756
    Processing helix  chain 'A' and resid 787 through 791
      removed outlier: 3.639A  pdb=" N   GLU A 791 " --> pdb=" O   ARG A 788 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 811 through 823
      removed outlier: 3.509A  pdb=" N   GLU A 815 " --> pdb=" O   LYS A 811 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   LYS A 821 " --> pdb=" O   ARG A 817 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ASP A 823 " --> pdb=" O   LEU A 819 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 872 through 885
      removed outlier: 3.509A  pdb=" N   GLU A 885 " --> pdb=" O   LYS A 881 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 886 through 888
      No H-bonds generated for 'chain 'A' and resid 886 through 888'
    Processing helix  chain 'A' and resid 889 through 919
    Processing helix  chain 'A' and resid 939 through 954
    Processing helix  chain 'A' and resid 1020 through 1030
    Processing helix  chain 'A' and resid 1091 through 1103
    Processing helix  chain 'A' and resid 1111 through 1118
    Processing helix  chain 'A' and resid 1120 through 1136
      removed outlier: 4.031A  pdb=" N   TYR A1124 " --> pdb=" O   ASP A1120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1163 through 1170
      removed outlier: 3.757A  pdb=" N   TYR A1167 " --> pdb=" O   ASP A1163 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ALA A1169 " --> pdb=" O   ARG A1165 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   GLN A1170 " --> pdb=" O   ASN A1166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1178 through 1201
      removed outlier: 3.673A  pdb=" N   LEU A1192 " --> pdb=" O   ALA A1188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1202 through 1206
    Processing sheet with id=AA1, first strand: chain 'A' and resid 545 through 549
      removed outlier: 3.583A  pdb=" N   LYS A 552 " --> pdb=" O   TYR A 549 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   TYR A 553 " --> pdb=" O   ILE A 704 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   LYS A  20 " --> pdb=" O   TYR A 705 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 545 through 549
      removed outlier: 3.583A  pdb=" N   LYS A 552 " --> pdb=" O   TYR A 549 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   TYR A 553 " --> pdb=" O   ILE A 704 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   LYS A  20 " --> pdb=" O   TYR A 705 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 582 through 583
    Processing sheet with id=AA4, first strand: chain 'A' and resid 841 through 844
      removed outlier: 6.287A  pdb=" N   ILE A 841 " --> pdb=" O   GLN A 853 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   GLN A 853 " --> pdb=" O   ILE A 841 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   VAL A 843 " --> pdb=" O   VAL A 851 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 858 through 862
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1031 through 1037
      removed outlier: 6.294A  pdb=" N   PHE A1031 " --> pdb=" O   ASP A1048 " (cutoff:3.500A)
      removed outlier: 6.003A  pdb=" N   ASP A1048 " --> pdb=" O   PHE A1031 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1070 through 1073
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1138 through 1139

    362 hydrogen bonds defined for protein.
    1017 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      14 hydrogen bonds
      24 hydrogen bond angles
      0 basepair planarities
      6 basepair parallelities
      13 stacking parallelities
  Total time for adding SS restraints: 1.82

  Time building geometry restraints manager: 1.06 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1614
        1.32 -     1.44: 2806
        1.44 -     1.56: 5350
        1.56 -     1.69: 54
        1.69 -     1.81: 40
  Bond restraints: 9864
  Sorted by residual:
  bond pdb=" C   ASN A1070 "
       pdb=" O   ASN A1070 "
    ideal  model  delta    sigma   weight residual
    1.236  1.380 -0.145 1.21e-02 6.83e+03 1.43e+02
  bond pdb=" C   HIS A 714 "
       pdb=" O   HIS A 714 "
    ideal  model  delta    sigma   weight residual
    1.236  1.381 -0.145 1.32e-02 5.74e+03 1.21e+02
  bond pdb=" C   ASN A1070 "
       pdb=" CA BASN A1070 "
    ideal  model  delta    sigma   weight residual
    1.522  1.619 -0.097 1.20e-02 6.94e+03 6.52e+01
  bond pdb=" C   ASN A1070 "
       pdb=" CA AASN A1070 "
    ideal  model  delta    sigma   weight residual
    1.522  1.618 -0.096 1.20e-02 6.94e+03 6.44e+01
  bond pdb=" C   HIS A 714 "
       pdb=" CA BHIS A 714 "
    ideal  model  delta    sigma   weight residual
    1.522  1.621 -0.099 1.39e-02 5.18e+03 5.05e+01
  ... (remaining 9859 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.87: 13299
        5.87 -    11.73: 110
       11.73 -    17.60: 17
       17.60 -    23.46: 0
       23.46 -    29.33: 1
  Bond angle restraints: 13427
  Sorted by residual:
  angle pdb=" O   ASN A1070 "
        pdb=" C   ASN A1070 "
        pdb=" CA AASN A1070 "
      ideal   model   delta    sigma   weight residual
     120.38  136.11  -15.73 1.09e+00 8.42e-01 2.08e+02
  angle pdb=" O   ASN A1070 "
        pdb=" C   ASN A1070 "
        pdb=" CA BASN A1070 "
      ideal   model   delta    sigma   weight residual
     120.38  136.08  -15.70 1.09e+00 8.42e-01 2.08e+02
  angle pdb=" N   GLU A1220 "
        pdb=" CA  GLU A1220 "
        pdb=" C   GLU A1220 "
      ideal   model   delta    sigma   weight residual
     110.80   81.47   29.33 2.13e+00 2.20e-01 1.90e+02
  angle pdb=" O   HIS A 714 "
        pdb=" C   HIS A 714 "
        pdb=" CA AHIS A 714 "
      ideal   model   delta    sigma   weight residual
     119.31  135.76  -16.45 1.24e+00 6.50e-01 1.76e+02
  angle pdb=" O   HIS A 714 "
        pdb=" C   HIS A 714 "
        pdb=" CA BHIS A 714 "
      ideal   model   delta    sigma   weight residual
     119.31  135.75  -16.44 1.24e+00 6.50e-01 1.76e+02
  ... (remaining 13422 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.64: 5155
       35.64 -    71.27: 776
       71.27 -   106.90: 24
      106.90 -   142.54: 0
      142.54 -   178.17: 2
  Dihedral angle restraints: 5957
    sinusoidal: 2625
      harmonic: 3332
  Sorted by residual:
  dihedral pdb=" O4'   U G  16 "
           pdb=" C1'   U G  16 "
           pdb=" N1    U G  16 "
           pdb=" C2    U G  16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   55.01  176.99     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" C   THR A 776 "
           pdb=" N   THR A 776 "
           pdb=" CA  THR A 776 "
           pdb=" CB  THR A 776 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -137.94   15.94     0      2.50e+00 1.60e-01 4.07e+01
  dihedral pdb=" C   GLU A1220 "
           pdb=" N   GLU A1220 "
           pdb=" CA  GLU A1220 "
           pdb=" CB  GLU A1220 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -107.94  -14.66     0      2.50e+00 1.60e-01 3.44e+01
  ... (remaining 5954 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.127: 1240
       0.127 -    0.254: 202
       0.254 -    0.381: 30
       0.381 -    0.508: 4
       0.508 -    0.635: 3
  Chirality restraints: 1479
  Sorted by residual:
  chirality pdb=" C3'   A G  14 "
            pdb=" C4'   A G  14 "
            pdb=" O3'   A G  14 "
            pdb=" C2'   A G  14 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.11   -0.63 2.00e-01 2.50e+01 1.01e+01
  chirality pdb=" CA  THR A 776 "
            pdb=" N   THR A 776 "
            pdb=" C   THR A 776 "
            pdb=" CB  THR A 776 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    1.94    0.58 2.00e-01 2.50e+01 8.55e+00
  chirality pdb=" CA  LYS A 267 "
            pdb=" N   LYS A 267 "
            pdb=" C   LYS A 267 "
            pdb=" CB  LYS A 267 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.93    0.58 2.00e-01 2.50e+01 8.53e+00
  ... (remaining 1476 not shown)

  Planarity restraints: 1632
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 270 "   -0.058 5.00e-02 4.00e+02   8.78e-02 1.23e+01
        pdb=" N   PRO A 271 "    0.152 5.00e-02 4.00e+02
        pdb=" CA  PRO A 271 "   -0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO A 271 "   -0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 128 "   -0.041 5.00e-02 4.00e+02   6.21e-02 6.16e+00
        pdb=" N   PRO A 129 "    0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO A 129 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 129 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 825 "   -0.034 5.00e-02 4.00e+02   5.14e-02 4.22e+00
        pdb=" N   PRO A 826 "    0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO A 826 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 826 "   -0.029 5.00e-02 4.00e+02
  ... (remaining 1629 not shown)

  Histogram of nonbonded interaction distances:
        1.06 -     1.83: 24
        1.83 -     2.60: 283
        2.60 -     3.36: 12606
        3.36 -     4.13: 29808
        4.13 -     4.90: 48917
  Nonbonded interactions: 91638
  Sorted by model distance:
  nonbonded pdb=" N   GLU A1039 "
            pdb=" OE1 GLU A1039 "
     model   vdw
     1.061 3.120
  nonbonded pdb=" CG1 VAL A 303 "
            pdb=" O   THR A 307 "
     model   vdw
     1.112 3.460
  nonbonded pdb=" O   ASN A 145 "
            pdb=" N   PHE A 147 "
     model   vdw
     1.126 3.120
  nonbonded pdb=" CG2 ILE A 240 "
            pdb=" O   GLY A 254 "
     model   vdw
     1.164 3.460
  nonbonded pdb=" CE2 PHE A 220 "
            pdb=" CD1 LEU A 255 "
     model   vdw
     1.212 3.760
  ... (remaining 91633 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=0.47 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             11.560
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     11.990
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:6.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5901
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      :  0.009   0.189   9866  Z= 0.665
  Angle     :  1.512  29.325  13427  Z= 1.013
  Chirality :  0.101   0.635   1479
  Planarity :  0.005   0.088   1632
  Dihedral  : 26.635 178.173   3811
  Min Nonbonded Distance : 1.061

Molprobity Statistics.
  All-atom Clashscore : 37.33
  Ramachandran Plot:
    Outliers :  3.68 %
    Allowed  : 16.35 %
    Favored  : 79.96 %
  Rotamer:
    Outliers : 44.05 %
    Allowed  : 18.38 %
    Favored  : 37.58 %
  Cbeta Deviations :  0.56 %
  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: -5.01 (0.20), residues: 1115
  helix: -2.75 (0.18), residues: 454
  sheet: -4.25 (0.39), residues: 113
  loop : -3.65 (0.22), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 747 
 TYR   0.022   0.002   TYR A1185 
 PHE   0.025   0.003   PHE A 521 
 TRP   0.009   0.002   TRP A 890 
 HIS   0.003   0.001   HIS A 370 

Details of bonding type rmsd
  covalent geometry    : bond        0.00863 ( 9864)
  covalent geometry    : angle       1.51244 (13427)
  hydrogen bonds       : bond        0.21004 (  357)
  hydrogen bonds       : angle       9.38872 ( 1041)
  Misc. bond           : bond        0.13853 (    2)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  692 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 429
    poor density    : 263
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 LYS cc_start: 0.6905 (OUTLIER) cc_final: 0.6567 (mmmt)
REVERT: A   48 LYS cc_start: 0.5835 (OUTLIER) cc_final: 0.5515 (tttt)
REVERT: A   61 PHE cc_start: 0.6138 (OUTLIER) cc_final: 0.5313 (t80)
REVERT: A   73 ASN cc_start: 0.1051 (OUTLIER) cc_final: 0.0436 (t0)
REVERT: A   87 THR cc_start: 0.3857 (OUTLIER) cc_final: 0.3606 (m)
REVERT: A  121 LYS cc_start: 0.6643 (OUTLIER) cc_final: 0.6152 (ptpt)
REVERT: A  256 ASN cc_start: 0.6687 (OUTLIER) cc_final: 0.6030 (t0)
REVERT: A  266 THR cc_start: 0.1224 (OUTLIER) cc_final: 0.0457 (p)
REVERT: A  286 SER cc_start: -0.3274 (OUTLIER) cc_final: -0.3696 (t)
REVERT: A  316 SER cc_start: 0.6226 (OUTLIER) cc_final: 0.5846 (t)
REVERT: A  324 LEU cc_start: 0.5824 (OUTLIER) cc_final: 0.5413 (mt)
REVERT: A  396 SER cc_start: 0.8511 (OUTLIER) cc_final: 0.8211 (t)
REVERT: A  398 GLU cc_start: 0.5900 (OUTLIER) cc_final: 0.5567 (mt-10)
REVERT: A  423 ASP cc_start: 0.6007 (m-30) cc_final: 0.5753 (m-30)
REVERT: A  485 SER cc_start: 0.7817 (OUTLIER) cc_final: 0.7531 (p)
REVERT: A  542 TYR cc_start: 0.2822 (OUTLIER) cc_final: 0.2271 (m-80)
REVERT: A  552 LYS cc_start: 0.6868 (OUTLIER) cc_final: 0.6630 (tppt)
REVERT: A  564 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7063 (ttmt)
REVERT: A  690 VAL cc_start: 0.8063 (t) cc_final: 0.7830 (t)
REVERT: A  807 LYS cc_start: 0.4791 (OUTLIER) cc_final: 0.4429 (ttmt)
REVERT: A  863 PHE cc_start: 0.6462 (OUTLIER) cc_final: 0.5481 (p90)
REVERT: A  897 LYS cc_start: 0.7645 (mtpt) cc_final: 0.7414 (mtpt)
REVERT: A  959 ASP cc_start: 0.6038 (OUTLIER) cc_final: 0.5832 (t0)
REVERT: A  967 THR cc_start: 0.7600 (OUTLIER) cc_final: 0.7363 (t)
REVERT: A 1020 SER cc_start: 0.8040 (p) cc_final: 0.7803 (m)
REVERT: A 1075 PHE cc_start: 0.4872 (p90) cc_final: 0.4586 (p90)
REVERT: A 1097 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7577 (pt0)
REVERT: A 1131 MET cc_start: 0.7853 (mmm) cc_final: 0.7558 (tpt)
REVERT: A 1155 LYS cc_start: 0.7431 (OUTLIER) cc_final: 0.7054 (ptpp)
REVERT: A 1214 SER cc_start: 0.7773 (OUTLIER) cc_final: 0.7358 (p)
  outliers start: 429
  outliers final: 54
  residues processed: 554
  average time/residue: 0.5217
  time to fit residues: 310.6704
Evaluate side-chains
  226 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 78
    poor density    : 148
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 LYS
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   16 THR
Chi-restraints excluded: chain A residue   48 LYS
Chi-restraints excluded: chain A residue   61 PHE
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue   73 ASN
Chi-restraints excluded: chain A residue   83 LYS
Chi-restraints excluded: chain A residue   87 THR
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  121 LYS
Chi-restraints excluded: chain A residue  127 ILE
Chi-restraints excluded: chain A residue  133 ASP
Chi-restraints excluded: chain A residue  165 GLU
Chi-restraints excluded: chain A residue  168 SER
Chi-restraints excluded: chain A residue  186 ASN
Chi-restraints excluded: chain A residue  187 MET
Chi-restraints excluded: chain A residue  190 PHE
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  240 ILE
Chi-restraints excluded: chain A residue  256 ASN
Chi-restraints excluded: chain A residue  259 ILE
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  288 SER
Chi-restraints excluded: chain A residue  296 SER
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  324 LEU
Chi-restraints excluded: chain A residue  325 PHE
Chi-restraints excluded: chain A residue  345 SER
Chi-restraints excluded: chain A residue  396 SER
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  418 ILE
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  485 SER
Chi-restraints excluded: chain A residue  542 TYR
Chi-restraints excluded: chain A residue  545 THR
Chi-restraints excluded: chain A residue  552 LYS
Chi-restraints excluded: chain A residue  564 LYS
Chi-restraints excluded: chain A residue  687 LYS
Chi-restraints excluded: chain A residue  695 GLU
Chi-restraints excluded: chain A residue  716 THR
Chi-restraints excluded: chain A residue  758 VAL
Chi-restraints excluded: chain A residue  765 ILE
Chi-restraints excluded: chain A residue  776 THR
Chi-restraints excluded: chain A residue  780 SER
Chi-restraints excluded: chain A residue  782 ASP
Chi-restraints excluded: chain A residue  802 ILE
Chi-restraints excluded: chain A residue  807 LYS
Chi-restraints excluded: chain A residue  837 ASN
Chi-restraints excluded: chain A residue  863 PHE
Chi-restraints excluded: chain A residue  904 ILE
Chi-restraints excluded: chain A residue  935 ARG
Chi-restraints excluded: chain A residue  959 ASP
Chi-restraints excluded: chain A residue  967 THR
Chi-restraints excluded: chain A residue  971 LEU
Chi-restraints excluded: chain A residue  996 ILE
Chi-restraints excluded: chain A residue 1019 THR
Chi-restraints excluded: chain A residue 1024 SER
Chi-restraints excluded: chain A residue 1029 SER
Chi-restraints excluded: chain A residue 1041 ASP
Chi-restraints excluded: chain A residue 1047 LEU
Chi-restraints excluded: chain A residue 1049 TYR
Chi-restraints excluded: chain A residue 1053 SER
Chi-restraints excluded: chain A residue 1068 TYR
Chi-restraints excluded: chain A residue 1097 GLU
Chi-restraints excluded: chain A residue 1118 GLN
Chi-restraints excluded: chain A residue 1119 SER
Chi-restraints excluded: chain A residue 1130 LEU
Chi-restraints excluded: chain A residue 1155 LYS
Chi-restraints excluded: chain A residue 1160 ILE
Chi-restraints excluded: chain A residue 1214 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    0.5980
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    1.9990
   chunk 113 optimal weight:    0.5980
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    3.9990
   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  30 ASN
A  33 ASN
A 200 HIS
A 211 ASN
A 226 ASN
A 268 GLN
** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 340 ASN
A 399 GLN
A 401 GLN
A 449 ASN
A 513 GLN
A 703 GLN
A 714 HIS    A
A 720 HIS
** A 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 797 HIS
A 822 HIS
** A 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 861 ASN
A 862 ASN
** A 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 895 ASN
A 909 HIS
A 941 GLN
A 955 ASN
A1012 ASN
A1186 ASN

Total number of N/Q/H flips: 24

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4735 r_free = 0.4735 target = 0.214717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4439 r_free = 0.4439 target = 0.176050 restraints weight = 38890.497|
|-----------------------------------------------------------------------------|
r_work (start): 0.4340 rms_B_bonded: 5.38
r_work: 0.4089 rms_B_bonded: 5.19 restraints_weight: 2.0000
r_work (final): 0.4089
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4113
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4113 r_free = 0.4113    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4113 r_free = 0.4113    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.4113
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6881
moved from start:          0.5122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.099   9866  Z= 0.232
  Angle     :  0.965  13.332  13427  Z= 0.504
  Chirality :  0.053   0.416   1479
  Planarity :  0.007   0.100   1632
  Dihedral  : 17.373 166.663   1766
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 23.38
  Ramachandran Plot:
    Outliers :  1.08 %
    Allowed  : 12.22 %
    Favored  : 86.70 %
  Rotamer:
    Outliers : 11.91 %
    Allowed  : 38.60 %
    Favored  : 49.49 %
  Cbeta Deviations :  0.09 %
  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: -3.43 (0.22), residues: 1115
  helix: -1.12 (0.22), residues: 453
  sheet: -3.66 (0.44), residues: 94
  loop : -3.09 (0.23), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 386 
 TYR   0.028   0.003   TYR A 854 
 PHE   0.023   0.003   PHE A 395 
 TRP   0.027   0.003   TRP A 890 
 HIS   0.008   0.002   HIS A 502 

Details of bonding type rmsd
  covalent geometry    : bond        0.00536 ( 9864)
  covalent geometry    : angle       0.96496 (13427)
  hydrogen bonds       : bond        0.05856 (  357)
  hydrogen bonds       : angle       6.41318 ( 1041)
  Misc. bond           : bond        0.01484 (    2)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 116
    poor density    : 146
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7343 (pp20)
REVERT: A   26 LYS cc_start: 0.7654 (mmmt) cc_final: 0.7293 (mmmt)
REVERT: A   48 LYS cc_start: 0.5670 (OUTLIER) cc_final: 0.5228 (tttt)
REVERT: A   61 PHE cc_start: 0.5056 (OUTLIER) cc_final: 0.4711 (t80)
REVERT: A  121 LYS cc_start: 0.6539 (OUTLIER) cc_final: 0.5835 (ptpt)
REVERT: A  182 ARG cc_start: 0.6345 (OUTLIER) cc_final: 0.5531 (mtp85)
REVERT: A  186 ASN cc_start: 0.5100 (OUTLIER) cc_final: 0.4854 (t0)
REVERT: A  253 LYS cc_start: 0.4513 (OUTLIER) cc_final: 0.4248 (pmtt)
REVERT: A  267 LYS cc_start: 0.3619 (OUTLIER) cc_final: 0.3279 (mppt)
REVERT: A  286 SER cc_start: -0.2916 (OUTLIER) cc_final: -0.3521 (t)
REVERT: A  321 LEU cc_start: 0.7021 (OUTLIER) cc_final: 0.6792 (mm)
REVERT: A  324 LEU cc_start: 0.6011 (OUTLIER) cc_final: 0.5732 (mt)
REVERT: A  325 PHE cc_start: 0.5370 (OUTLIER) cc_final: 0.4080 (m-10)
REVERT: A  414 LEU cc_start: 0.7019 (OUTLIER) cc_final: 0.6751 (tp)
REVERT: A  419 ILE cc_start: 0.7821 (mt) cc_final: 0.7236 (mp)
REVERT: A  423 ASP cc_start: 0.6446 (m-30) cc_final: 0.5995 (m-30)
REVERT: A  552 LYS cc_start: 0.6664 (mmtm) cc_final: 0.6342 (mppt)
REVERT: A  564 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.6643 (ttpt)
REVERT: A  680 VAL cc_start: 0.5364 (OUTLIER) cc_final: 0.5150 (p)
REVERT: A  686 SER cc_start: 0.5951 (OUTLIER) cc_final: 0.4638 (m)
REVERT: A  687 LYS cc_start: 0.7014 (OUTLIER) cc_final: 0.6802 (tttp)
REVERT: A  703 GLN cc_start: 0.5370 (OUTLIER) cc_final: 0.3782 (tt0)
REVERT: A  768 LYS cc_start: 0.6460 (tptp) cc_final: 0.5828 (mttt)
REVERT: A  769 ASN cc_start: 0.6515 (t0) cc_final: 0.5415 (t0)
REVERT: A  899 LEU cc_start: 0.7052 (OUTLIER) cc_final: 0.6725 (tp)
  outliers start: 116
  outliers final: 38
  residues processed: 242
  average time/residue: 0.4402
  time to fit residues: 116.4015
Evaluate side-chains
  175 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 118
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 GLU
Chi-restraints excluded: chain A residue   16 THR
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue   48 LYS
Chi-restraints excluded: chain A residue   61 PHE
Chi-restraints excluded: chain A residue  121 LYS
Chi-restraints excluded: chain A residue  127 ILE
Chi-restraints excluded: chain A residue  133 ASP
Chi-restraints excluded: chain A residue  165 GLU
Chi-restraints excluded: chain A residue  168 SER
Chi-restraints excluded: chain A residue  182 ARG
Chi-restraints excluded: chain A residue  183 TYR
Chi-restraints excluded: chain A residue  186 ASN
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  253 LYS
Chi-restraints excluded: chain A residue  267 LYS
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  288 SER
Chi-restraints excluded: chain A residue  290 TYR
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  324 LEU
Chi-restraints excluded: chain A residue  325 PHE
Chi-restraints excluded: chain A residue  345 SER
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  476 GLU
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  545 THR
Chi-restraints excluded: chain A residue  564 LYS
Chi-restraints excluded: chain A residue  680 VAL
Chi-restraints excluded: chain A residue  686 SER
Chi-restraints excluded: chain A residue  687 LYS
Chi-restraints excluded: chain A residue  703 GLN
Chi-restraints excluded: chain A residue  750 SER
Chi-restraints excluded: chain A residue  758 VAL
Chi-restraints excluded: chain A residue  776 THR
Chi-restraints excluded: chain A residue  782 ASP
Chi-restraints excluded: chain A residue  809 ILE
Chi-restraints excluded: chain A residue  812 ILE
Chi-restraints excluded: chain A residue  837 ASN
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  905 SER
Chi-restraints excluded: chain A residue  935 ARG
Chi-restraints excluded: chain A residue  971 LEU
Chi-restraints excluded: chain A residue 1019 THR
Chi-restraints excluded: chain A residue 1030 SER
Chi-restraints excluded: chain A residue 1047 LEU
Chi-restraints excluded: chain A residue 1049 TYR
Chi-restraints excluded: chain A residue 1067 SER
Chi-restraints excluded: chain A residue 1089 VAL
Chi-restraints excluded: chain A residue 1155 LYS
Chi-restraints excluded: chain A residue 1158 ASP
Chi-restraints excluded: chain A residue 1187 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 95 optimal weight:    4.9990
   chunk 111 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   chunk 65 optimal weight:    0.0570
   chunk 21 optimal weight:    7.9990
   chunk 40 optimal weight:    1.9990
   chunk 90 optimal weight:    0.6980
   chunk 66 optimal weight:    0.8980
   overall best weight:    0.7300

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

Flipped N/Q/H residues before XYZ refinement:
A  73 ASN
A 226 ASN
A 231 GLN
A 311 ASN
A 793 GLN
** A 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 862 ASN
** A 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4739 r_free = 0.4739 target = 0.217717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4474 r_free = 0.4474 target = 0.181714 restraints weight = 27607.438|
|-----------------------------------------------------------------------------|
r_work (start): 0.4365 rms_B_bonded: 3.79
r_work: 0.4124 rms_B_bonded: 4.45 restraints_weight: 0.5000
r_work (final): 0.4124
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4145
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4145 r_free = 0.4145    target_work(ls_wunit_k1) = 0.156         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4145 r_free = 0.4145    target_work(ls_wunit_k1) = 0.156         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.4145
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6864
moved from start:          0.5894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070   9866  Z= 0.193
  Angle     :  0.844  12.997  13427  Z= 0.437
  Chirality :  0.048   0.308   1479
  Planarity :  0.006   0.096   1632
  Dihedral  : 15.762 169.654   1673
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 19.64
  Ramachandran Plot:
    Outliers :  0.81 %
    Allowed  : 12.67 %
    Favored  : 86.52 %
  Rotamer:
    Outliers :  9.03 %
    Allowed  : 39.32 %
    Favored  : 51.64 %
  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: -2.91 (0.23), residues: 1115
  helix: -0.56 (0.23), residues: 443
  sheet: -3.47 (0.43), residues: 94
  loop : -2.86 (0.24), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 385 
 TYR   0.024   0.002   TYR A 854 
 PHE   0.034   0.002   PHE A 220 
 TRP   0.033   0.002   TRP A 890 
 HIS   0.009   0.002   HIS A 502 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 ( 9864)
  covalent geometry    : angle       0.84407 (13427)
  hydrogen bonds       : bond        0.05132 (  357)
  hydrogen bonds       : angle       5.93044 ( 1041)
  Misc. bond           : bond        0.01252 (    2)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 86
    poor density    : 131
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 PHE cc_start: 0.5082 (t80) cc_final: 0.4845 (t80)
REVERT: A   86 ARG cc_start: 0.4353 (OUTLIER) cc_final: 0.2891 (mtp180)
REVERT: A   95 GLU cc_start: 0.4735 (OUTLIER) cc_final: 0.4508 (tt0)
REVERT: A  121 LYS cc_start: 0.6587 (OUTLIER) cc_final: 0.5950 (ptpt)
REVERT: A  186 ASN cc_start: 0.5827 (OUTLIER) cc_final: 0.5151 (t0)
REVERT: A  253 LYS cc_start: 0.4167 (OUTLIER) cc_final: 0.3772 (pmtt)
REVERT: A  267 LYS cc_start: 0.3695 (OUTLIER) cc_final: 0.3371 (mppt)
REVERT: A  325 PHE cc_start: 0.5263 (OUTLIER) cc_final: 0.3905 (m-10)
REVERT: A  402 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7545 (tp30)
REVERT: A  412 GLU cc_start: 0.7292 (mp0) cc_final: 0.7019 (pp20)
REVERT: A  419 ILE cc_start: 0.7772 (mt) cc_final: 0.7301 (mm)
REVERT: A  423 ASP cc_start: 0.6533 (m-30) cc_final: 0.6122 (m-30)
REVERT: A  503 ILE cc_start: 0.6528 (OUTLIER) cc_final: 0.5947 (mt)
REVERT: A  564 LYS cc_start: 0.7615 (OUTLIER) cc_final: 0.6643 (ttpt)
REVERT: A  686 SER cc_start: 0.5976 (OUTLIER) cc_final: 0.4861 (m)
REVERT: A  768 LYS cc_start: 0.6362 (tptp) cc_final: 0.5790 (mttm)
REVERT: A  769 ASN cc_start: 0.6509 (t0) cc_final: 0.5447 (t0)
REVERT: A  787 LYS cc_start: 0.6815 (OUTLIER) cc_final: 0.6594 (pttt)
REVERT: A  866 ILE cc_start: 0.8027 (OUTLIER) cc_final: 0.7496 (mp)
  outliers start: 86
  outliers final: 28
  residues processed: 204
  average time/residue: 0.4658
  time to fit residues: 103.9765
Evaluate side-chains
  146 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 105
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue   86 ARG
Chi-restraints excluded: chain A residue   95 GLU
Chi-restraints excluded: chain A residue  121 LYS
Chi-restraints excluded: chain A residue  133 ASP
Chi-restraints excluded: chain A residue  186 ASN
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  253 LYS
Chi-restraints excluded: chain A residue  267 LYS
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  290 TYR
Chi-restraints excluded: chain A residue  325 PHE
Chi-restraints excluded: chain A residue  345 SER
Chi-restraints excluded: chain A residue  369 ILE
Chi-restraints excluded: chain A residue  402 GLU
Chi-restraints excluded: chain A residue  476 GLU
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  503 ILE
Chi-restraints excluded: chain A residue  564 LYS
Chi-restraints excluded: chain A residue  570 ASP
Chi-restraints excluded: chain A residue  686 SER
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  750 SER
Chi-restraints excluded: chain A residue  758 VAL
Chi-restraints excluded: chain A residue  776 THR
Chi-restraints excluded: chain A residue  787 LYS
Chi-restraints excluded: chain A residue  809 ILE
Chi-restraints excluded: chain A residue  837 ASN
Chi-restraints excluded: chain A residue  866 ILE
Chi-restraints excluded: chain A residue  891 THR
Chi-restraints excluded: chain A residue  905 SER
Chi-restraints excluded: chain A residue  935 ARG
Chi-restraints excluded: chain A residue  971 LEU
Chi-restraints excluded: chain A residue 1019 THR
Chi-restraints excluded: chain A residue 1030 SER
Chi-restraints excluded: chain A residue 1047 LEU
Chi-restraints excluded: chain A residue 1155 LYS
Chi-restraints excluded: chain A residue 1158 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 30 optimal weight:    0.7980
   chunk 64 optimal weight:    0.6980
   chunk 79 optimal weight:    0.7980
   chunk 5 optimal weight:    8.9990
   chunk 92 optimal weight:    0.1980
   chunk 51 optimal weight:    1.9990
   chunk 68 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9990
   chunk 90 optimal weight:    0.7980
   chunk 47 optimal weight:    0.0010
   chunk 81 optimal weight:    0.5980
   overall best weight:    0.4186

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

Flipped N/Q/H residues before XYZ refinement:
A  76 ASN
** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 862 ASN
** A 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4766 r_free = 0.4766 target = 0.221191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4525 r_free = 0.4525 target = 0.186784 restraints weight = 33470.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.4403 rms_B_bonded: 4.51
r_work: 0.4129 rms_B_bonded: 4.89 restraints_weight: 0.5000
r_work (final): 0.4129
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4150
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4150 r_free = 0.4150    target_work(ls_wunit_k1) = 0.157         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4150 r_free = 0.4150    target_work(ls_wunit_k1) = 0.157         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.4150
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6836
moved from start:          0.6342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   9866  Z= 0.170
  Angle     :  0.801  11.986  13427  Z= 0.413
  Chirality :  0.047   0.269   1479
  Planarity :  0.005   0.089   1632
  Dihedral  : 15.323 171.542   1645
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 18.84
  Ramachandran Plot:
    Outliers :  0.81 %
    Allowed  : 11.59 %
    Favored  : 87.60 %
  Rotamer:
    Outliers :  6.47 %
    Allowed  : 41.48 %
    Favored  : 52.05 %
  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: -2.62 (0.24), residues: 1115
  helix: -0.24 (0.24), residues: 449
  sheet: -3.24 (0.44), residues: 94
  loop : -2.81 (0.24), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A1071 
 TYR   0.021   0.002   TYR A 854 
 PHE   0.034   0.002   PHE A 220 
 TRP   0.023   0.001   TRP A 890 
 HIS   0.013   0.002   HIS A 502 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 9864)
  covalent geometry    : angle       0.80059 (13427)
  hydrogen bonds       : bond        0.04595 (  357)
  hydrogen bonds       : angle       5.47831 ( 1041)
  Misc. bond           : bond        0.01224 (    2)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 116
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 ARG cc_start: 0.4420 (OUTLIER) cc_final: 0.2756 (mtp180)
REVERT: A   95 GLU cc_start: 0.4929 (OUTLIER) cc_final: 0.4682 (tt0)
REVERT: A  121 LYS cc_start: 0.6634 (OUTLIER) cc_final: 0.6017 (ptpt)
REVERT: A  186 ASN cc_start: 0.5516 (OUTLIER) cc_final: 0.5044 (t160)
REVERT: A  267 LYS cc_start: 0.3839 (OUTLIER) cc_final: 0.3610 (mppt)
REVERT: A  325 PHE cc_start: 0.5200 (OUTLIER) cc_final: 0.3731 (m-10)
REVERT: A  402 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7535 (tp30)
REVERT: A  503 ILE cc_start: 0.6500 (OUTLIER) cc_final: 0.5947 (mt)
REVERT: A  562 TYR cc_start: 0.5244 (OUTLIER) cc_final: 0.4966 (t80)
REVERT: A  564 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.6610 (ttpt)
REVERT: A  678 TYR cc_start: 0.2014 (OUTLIER) cc_final: 0.1721 (t80)
REVERT: A  686 SER cc_start: 0.5825 (OUTLIER) cc_final: 0.5021 (m)
REVERT: A  687 LYS cc_start: 0.7787 (tttp) cc_final: 0.7297 (tttp)
REVERT: A  691 ASP cc_start: 0.7500 (p0) cc_final: 0.7003 (m-30)
REVERT: A  768 LYS cc_start: 0.6283 (tptp) cc_final: 0.5742 (mttm)
REVERT: A  769 ASN cc_start: 0.6492 (t0) cc_final: 0.5407 (t0)
REVERT: A  787 LYS cc_start: 0.6720 (OUTLIER) cc_final: 0.6518 (pttt)
REVERT: A 1131 MET cc_start: 0.7735 (mmm) cc_final: 0.7470 (tpt)
  outliers start: 61
  outliers final: 24
  residues processed: 168
  average time/residue: 0.4765
  time to fit residues: 87.6228
Evaluate side-chains
  134 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 97
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue   86 ARG
Chi-restraints excluded: chain A residue   95 GLU
Chi-restraints excluded: chain A residue  121 LYS
Chi-restraints excluded: chain A residue  133 ASP
Chi-restraints excluded: chain A residue  176 ILE
Chi-restraints excluded: chain A residue  186 ASN
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  267 LYS
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  290 TYR
Chi-restraints excluded: chain A residue  325 PHE
Chi-restraints excluded: chain A residue  402 GLU
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  503 ILE
Chi-restraints excluded: chain A residue  562 TYR
Chi-restraints excluded: chain A residue  564 LYS
Chi-restraints excluded: chain A residue  570 ASP
Chi-restraints excluded: chain A residue  678 TYR
Chi-restraints excluded: chain A residue  686 SER
Chi-restraints excluded: chain A residue  704 ILE
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  750 SER
Chi-restraints excluded: chain A residue  758 VAL
Chi-restraints excluded: chain A residue  776 THR
Chi-restraints excluded: chain A residue  787 LYS
Chi-restraints excluded: chain A residue  809 ILE
Chi-restraints excluded: chain A residue  812 ILE
Chi-restraints excluded: chain A residue  905 SER
Chi-restraints excluded: chain A residue  935 ARG
Chi-restraints excluded: chain A residue  971 LEU
Chi-restraints excluded: chain A residue  972 LYS
Chi-restraints excluded: chain A residue 1019 THR
Chi-restraints excluded: chain A residue 1049 TYR
Chi-restraints excluded: chain A residue 1155 LYS
Chi-restraints excluded: chain A residue 1158 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 105 optimal weight:    0.5980
   chunk 98 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9990
   chunk 4 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   overall best weight:    1.3188

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

Flipped N/Q/H residues before XYZ refinement:
** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 582 ASN
A 862 ASN
** A 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1197 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4697 r_free = 0.4697 target = 0.210852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4416 r_free = 0.4416 target = 0.174619 restraints weight = 37014.818|
|-----------------------------------------------------------------------------|
r_work (start): 0.4331 rms_B_bonded: 5.20
r_work: 0.4046 rms_B_bonded: 5.01 restraints_weight: 2.0000
r_work (final): 0.4046
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4065
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4065 r_free = 0.4065    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4065 r_free = 0.4065    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.4065
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6995
moved from start:          0.6634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062   9866  Z= 0.211
  Angle     :  0.827  11.557  13427  Z= 0.425
  Chirality :  0.048   0.258   1479
  Planarity :  0.005   0.085   1632
  Dihedral  : 14.975 164.993   1638
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 18.84
  Ramachandran Plot:
    Outliers :  0.81 %
    Allowed  : 11.95 %
    Favored  : 87.24 %
  Rotamer:
    Outliers :  6.47 %
    Allowed  : 41.17 %
    Favored  : 52.36 %
  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: -2.53 (0.24), residues: 1115
  helix: -0.16 (0.24), residues: 451
  sheet: -3.04 (0.42), residues: 100
  loop : -2.79 (0.25), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A1071 
 TYR   0.028   0.002   TYR A 903 
 PHE   0.028   0.003   PHE A 220 
 TRP   0.020   0.002   TRP A 890 
 HIS   0.009   0.002   HIS A 502 

Details of bonding type rmsd
  covalent geometry    : bond        0.00471 ( 9864)
  covalent geometry    : angle       0.82652 (13427)
  hydrogen bonds       : bond        0.05120 (  357)
  hydrogen bonds       : angle       5.43526 ( 1041)
  Misc. bond           : bond        0.01267 (    2)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 110
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 PHE cc_start: 0.5536 (t80) cc_final: 0.4904 (t80)
REVERT: A   86 ARG cc_start: 0.4563 (OUTLIER) cc_final: 0.2721 (mtp180)
REVERT: A  121 LYS cc_start: 0.6638 (OUTLIER) cc_final: 0.5972 (ptpt)
REVERT: A  186 ASN cc_start: 0.5373 (OUTLIER) cc_final: 0.4875 (t160)
REVERT: A  187 MET cc_start: 0.2574 (OUTLIER) cc_final: 0.0355 (tmm)
REVERT: A  260 ASN cc_start: 0.7981 (t0) cc_final: 0.7410 (m-40)
REVERT: A  267 LYS cc_start: 0.3949 (OUTLIER) cc_final: 0.3734 (mppt)
REVERT: A  325 PHE cc_start: 0.5365 (OUTLIER) cc_final: 0.3829 (m-10)
REVERT: A  503 ILE cc_start: 0.6476 (OUTLIER) cc_final: 0.5774 (mt)
REVERT: A  564 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.6659 (ttpt)
REVERT: A  678 TYR cc_start: 0.2061 (OUTLIER) cc_final: 0.1740 (t80)
REVERT: A  686 SER cc_start: 0.5906 (OUTLIER) cc_final: 0.5163 (m)
REVERT: A  687 LYS cc_start: 0.7865 (tttp) cc_final: 0.7513 (tttp)
REVERT: A  768 LYS cc_start: 0.6471 (tptp) cc_final: 0.5952 (mttm)
REVERT: A  769 ASN cc_start: 0.6832 (t0) cc_final: 0.6429 (t0)
REVERT: A  972 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7121 (ttpt)
  outliers start: 61
  outliers final: 27
  residues processed: 162
  average time/residue: 0.5015
  time to fit residues: 88.4658
Evaluate side-chains
  133 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 95
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue   86 ARG
Chi-restraints excluded: chain A residue  121 LYS
Chi-restraints excluded: chain A residue  133 ASP
Chi-restraints excluded: chain A residue  176 ILE
Chi-restraints excluded: chain A residue  186 ASN
Chi-restraints excluded: chain A residue  187 MET
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  267 LYS
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  290 TYR
Chi-restraints excluded: chain A residue  305 ARG
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  325 PHE
Chi-restraints excluded: chain A residue  476 GLU
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  503 ILE
Chi-restraints excluded: chain A residue  564 LYS
Chi-restraints excluded: chain A residue  570 ASP
Chi-restraints excluded: chain A residue  582 ASN
Chi-restraints excluded: chain A residue  678 TYR
Chi-restraints excluded: chain A residue  686 SER
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  750 SER
Chi-restraints excluded: chain A residue  758 VAL
Chi-restraints excluded: chain A residue  776 THR
Chi-restraints excluded: chain A residue  809 ILE
Chi-restraints excluded: chain A residue  905 SER
Chi-restraints excluded: chain A residue  935 ARG
Chi-restraints excluded: chain A residue  971 LEU
Chi-restraints excluded: chain A residue  972 LYS
Chi-restraints excluded: chain A residue 1004 ILE
Chi-restraints excluded: chain A residue 1049 TYR
Chi-restraints excluded: chain A residue 1155 LYS
Chi-restraints excluded: chain A residue 1158 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 40 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   chunk 69 optimal weight:    2.9990
   chunk 56 optimal weight:   10.0000
   chunk 62 optimal weight:    0.6980
   chunk 29 optimal weight:    0.3980
   chunk 26 optimal weight:    5.9990
   chunk 58 optimal weight:   10.0000
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.8186

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

Flipped N/Q/H residues before XYZ refinement:
** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4612 r_free = 0.4612 target = 0.210330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.171336 restraints weight = 41736.968|
|-----------------------------------------------------------------------------|
r_work (start): 0.4223 rms_B_bonded: 5.66
r_work (final): 0.4223
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4226
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4226 r_free = 0.4226    target_work(ls_wunit_k1) = 0.169         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4226 r_free = 0.4226    target_work(ls_wunit_k1) = 0.169         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.4226
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6638
moved from start:          0.6930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.077   9866  Z= 0.179
  Angle     :  0.791  12.288  13427  Z= 0.407
  Chirality :  0.047   0.347   1479
  Planarity :  0.005   0.085   1632
  Dihedral  : 14.952 168.348   1637
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 17.87
  Ramachandran Plot:
    Outliers :  0.81 %
    Allowed  : 10.87 %
    Favored  : 88.32 %
  Rotamer:
    Outliers :  6.26 %
    Allowed  : 41.48 %
    Favored  : 52.26 %
  Cbeta Deviations :  0.09 %
  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: -2.40 (0.24), residues: 1115
  helix: -0.03 (0.24), residues: 462
  sheet: -3.12 (0.41), residues: 110
  loop : -2.72 (0.25), residues: 543

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A1071 
 TYR   0.026   0.002   TYR A 903 
 PHE   0.029   0.002   PHE A 220 
 TRP   0.019   0.001   TRP A 890 
 HIS   0.007   0.001   HIS A 502 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 9864)
  covalent geometry    : angle       0.79141 (13427)
  hydrogen bonds       : bond        0.04632 (  357)
  hydrogen bonds       : angle       5.20844 ( 1041)
  Misc. bond           : bond        0.01310 (    2)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 107
  time to evaluate  : 0.430 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6966 (pp20)
REVERT: A   61 PHE cc_start: 0.5942 (t80) cc_final: 0.5501 (t80)
REVERT: A   86 ARG cc_start: 0.4186 (OUTLIER) cc_final: 0.2425 (mtp180)
REVERT: A  121 LYS cc_start: 0.6544 (OUTLIER) cc_final: 0.5951 (ptpt)
REVERT: A  186 ASN cc_start: 0.5468 (OUTLIER) cc_final: 0.5183 (t0)
REVERT: A  187 MET cc_start: 0.1416 (tpt) cc_final: 0.0922 (tmm)
REVERT: A  260 ASN cc_start: 0.7950 (t0) cc_final: 0.7509 (m-40)
REVERT: A  276 LEU cc_start: 0.6679 (OUTLIER) cc_final: 0.6068 (mt)
REVERT: A  325 PHE cc_start: 0.5066 (OUTLIER) cc_final: 0.3760 (m-10)
REVERT: A  402 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7539 (tp30)
REVERT: A  503 ILE cc_start: 0.6516 (OUTLIER) cc_final: 0.5601 (mt)
REVERT: A  564 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.6748 (ttpt)
REVERT: A  686 SER cc_start: 0.5384 (OUTLIER) cc_final: 0.4814 (m)
REVERT: A  687 LYS cc_start: 0.7740 (tttp) cc_final: 0.7277 (tttp)
REVERT: A  691 ASP cc_start: 0.7462 (p0) cc_final: 0.7028 (m-30)
REVERT: A  768 LYS cc_start: 0.6097 (tptp) cc_final: 0.5789 (mttm)
REVERT: A  769 ASN cc_start: 0.6148 (t0) cc_final: 0.5833 (t0)
REVERT: A  967 THR cc_start: 0.7727 (m) cc_final: 0.7520 (m)
REVERT: A  972 LYS cc_start: 0.7428 (OUTLIER) cc_final: 0.6854 (ttpt)
  outliers start: 59
  outliers final: 25
  residues processed: 158
  average time/residue: 0.4622
  time to fit residues: 80.0370
Evaluate side-chains
  134 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 98
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 GLU
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue   86 ARG
Chi-restraints excluded: chain A residue  121 LYS
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  133 ASP
Chi-restraints excluded: chain A residue  161 MET
Chi-restraints excluded: chain A residue  186 ASN
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  290 TYR
Chi-restraints excluded: chain A residue  305 ARG
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  325 PHE
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  402 GLU
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  503 ILE
Chi-restraints excluded: chain A residue  545 THR
Chi-restraints excluded: chain A residue  564 LYS
Chi-restraints excluded: chain A residue  570 ASP
Chi-restraints excluded: chain A residue  686 SER
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  750 SER
Chi-restraints excluded: chain A residue  758 VAL
Chi-restraints excluded: chain A residue  776 THR
Chi-restraints excluded: chain A residue  809 ILE
Chi-restraints excluded: chain A residue  812 ILE
Chi-restraints excluded: chain A residue  905 SER
Chi-restraints excluded: chain A residue  935 ARG
Chi-restraints excluded: chain A residue  971 LEU
Chi-restraints excluded: chain A residue  972 LYS
Chi-restraints excluded: chain A residue 1155 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 107 optimal weight:    0.9990
   chunk 10 optimal weight:    9.9990
   chunk 104 optimal weight:    0.8980
   chunk 84 optimal weight:    1.9990
   chunk 8 optimal weight:    6.9990
   chunk 6 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 7 optimal weight:    9.9990
   chunk 64 optimal weight:    3.9990
   overall best weight:    1.3788

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

Flipped N/Q/H residues before XYZ refinement:
A  63 ASN
A  76 ASN
** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 582 ASN
A 862 ASN
** A 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4591 r_free = 0.4591 target = 0.207834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.167835 restraints weight = 31446.693|
|-----------------------------------------------------------------------------|
r_work (start): 0.4181 rms_B_bonded: 4.85
r_work: 0.3950 rms_B_bonded: 4.74 restraints_weight: 0.5000
r_work (final): 0.3950
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3944
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3944 r_free = 0.3944    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3944 r_free = 0.3944    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3944
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7002
moved from start:          0.7091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065   9866  Z= 0.214
  Angle     :  0.821  12.151  13427  Z= 0.422
  Chirality :  0.048   0.332   1479
  Planarity :  0.005   0.085   1632
  Dihedral  : 14.923 164.711   1637
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 19.32
  Ramachandran Plot:
    Outliers :  0.72 %
    Allowed  : 11.95 %
    Favored  : 87.33 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 42.92 %
    Favored  : 52.05 %
  Cbeta Deviations :  0.09 %
  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: -2.38 (0.24), residues: 1115
  helix: -0.06 (0.24), residues: 463
  sheet: -2.73 (0.44), residues: 95
  loop : -2.79 (0.24), residues: 557

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A1071 
 TYR   0.037   0.002   TYR A 903 
 PHE   0.024   0.002   PHE A 220 
 TRP   0.019   0.002   TRP A 890 
 HIS   0.006   0.001   HIS A 502 

Details of bonding type rmsd
  covalent geometry    : bond        0.00481 ( 9864)
  covalent geometry    : angle       0.82128 (13427)
  hydrogen bonds       : bond        0.05031 (  357)
  hydrogen bonds       : angle       5.28180 ( 1041)
  Misc. bond           : bond        0.01268 (    2)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 101
  time to evaluate  : 0.462 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.7119 (pp20)
REVERT: A   61 PHE cc_start: 0.5565 (t80) cc_final: 0.5167 (t80)
REVERT: A  121 LYS cc_start: 0.6589 (OUTLIER) cc_final: 0.5899 (ptpt)
REVERT: A  186 ASN cc_start: 0.4802 (OUTLIER) cc_final: 0.4356 (t0)
REVERT: A  237 TYR cc_start: 0.7218 (t80) cc_final: 0.6456 (t80)
REVERT: A  260 ASN cc_start: 0.7987 (t0) cc_final: 0.7409 (m-40)
REVERT: A  276 LEU cc_start: 0.6666 (OUTLIER) cc_final: 0.6115 (mt)
REVERT: A  325 PHE cc_start: 0.5453 (OUTLIER) cc_final: 0.3828 (m-10)
REVERT: A  552 LYS cc_start: 0.6873 (mppt) cc_final: 0.6069 (mttm)
REVERT: A  686 SER cc_start: 0.5721 (OUTLIER) cc_final: 0.5187 (m)
REVERT: A  691 ASP cc_start: 0.7529 (p0) cc_final: 0.7000 (m-30)
REVERT: A  768 LYS cc_start: 0.6607 (tptp) cc_final: 0.6135 (mttm)
REVERT: A  769 ASN cc_start: 0.6782 (t0) cc_final: 0.6386 (t0)
REVERT: A  972 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7129 (ttpt)
  outliers start: 47
  outliers final: 27
  residues processed: 141
  average time/residue: 0.4251
  time to fit residues: 65.9525
Evaluate side-chains
  131 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 97
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 GLU
Chi-restraints excluded: chain A residue   16 THR
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue  121 LYS
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  133 ASP
Chi-restraints excluded: chain A residue  176 ILE
Chi-restraints excluded: chain A residue  186 ASN
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  290 TYR
Chi-restraints excluded: chain A residue  305 ARG
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  325 PHE
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  545 THR
Chi-restraints excluded: chain A residue  570 ASP
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain A residue  686 SER
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  750 SER
Chi-restraints excluded: chain A residue  758 VAL
Chi-restraints excluded: chain A residue  776 THR
Chi-restraints excluded: chain A residue  809 ILE
Chi-restraints excluded: chain A residue  812 ILE
Chi-restraints excluded: chain A residue  905 SER
Chi-restraints excluded: chain A residue  935 ARG
Chi-restraints excluded: chain A residue  971 LEU
Chi-restraints excluded: chain A residue  972 LYS
Chi-restraints excluded: chain A residue 1049 TYR
Chi-restraints excluded: chain A residue 1155 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 68 optimal weight:    3.9990
   chunk 66 optimal weight:    0.5980
   chunk 100 optimal weight:    5.9990
   chunk 112 optimal weight:    2.9990
   chunk 79 optimal weight:    0.7980
   chunk 8 optimal weight:    8.9990
   chunk 18 optimal weight:    7.9990
   chunk 78 optimal weight:    0.9990
   chunk 93 optimal weight:    0.3980
   chunk 0 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 582 ASN
** A 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 975 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 = 0.4617 r_free = 0.4617 target = 0.210202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.171520 restraints weight = 31471.645|
|-----------------------------------------------------------------------------|
r_work (start): 0.4220 rms_B_bonded: 4.76
r_work: 0.3987 rms_B_bonded: 4.62 restraints_weight: 0.5000
r_work (final): 0.3987
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4000
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4000 r_free = 0.4000    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4000 r_free = 0.4000    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.4000
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6913
moved from start:          0.7366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   9866  Z= 0.183
  Angle     :  0.803  13.745  13427  Z= 0.410
  Chirality :  0.047   0.331   1479
  Planarity :  0.005   0.080   1632
  Dihedral  : 14.862 168.075   1633
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 17.34
  Ramachandran Plot:
    Outliers :  0.72 %
    Allowed  : 10.06 %
    Favored  : 89.22 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 44.05 %
    Favored  : 51.54 %
  Cbeta Deviations :  0.09 %
  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: -2.25 (0.24), residues: 1115
  helix:  0.02 (0.24), residues: 462
  sheet: -2.47 (0.45), residues: 100
  loop : -2.72 (0.24), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A1071 
 TYR   0.032   0.002   TYR A 903 
 PHE   0.022   0.002   PHE A 220 
 TRP   0.018   0.001   TRP A 890 
 HIS   0.005   0.001   HIS A 502 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 ( 9864)
  covalent geometry    : angle       0.80348 (13427)
  hydrogen bonds       : bond        0.04543 (  357)
  hydrogen bonds       : angle       5.09509 ( 1041)
  Misc. bond           : bond        0.01221 (    2)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 103
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.7073 (pp20)
REVERT: A   61 PHE cc_start: 0.5410 (t80) cc_final: 0.5085 (t80)
REVERT: A  121 LYS cc_start: 0.6460 (OUTLIER) cc_final: 0.5802 (ptpt)
REVERT: A  186 ASN cc_start: 0.4555 (OUTLIER) cc_final: 0.4191 (t0)
REVERT: A  237 TYR cc_start: 0.7210 (t80) cc_final: 0.6446 (t80)
REVERT: A  260 ASN cc_start: 0.7944 (t0) cc_final: 0.7400 (m-40)
REVERT: A  276 LEU cc_start: 0.6657 (OUTLIER) cc_final: 0.6121 (mt)
REVERT: A  325 PHE cc_start: 0.5347 (OUTLIER) cc_final: 0.3657 (m-10)
REVERT: A  552 LYS cc_start: 0.6823 (mppt) cc_final: 0.6029 (mttm)
REVERT: A  686 SER cc_start: 0.5647 (OUTLIER) cc_final: 0.5219 (m)
REVERT: A  687 LYS cc_start: 0.7835 (tttp) cc_final: 0.7233 (tttp)
REVERT: A  691 ASP cc_start: 0.7506 (p0) cc_final: 0.7058 (m-30)
REVERT: A  768 LYS cc_start: 0.6467 (tptp) cc_final: 0.6034 (mttm)
REVERT: A  769 ASN cc_start: 0.6646 (t0) cc_final: 0.6248 (t0)
REVERT: A  972 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.6995 (ttpt)
  outliers start: 41
  outliers final: 28
  residues processed: 137
  average time/residue: 0.3832
  time to fit residues: 57.7353
Evaluate side-chains
  130 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 95
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 GLU
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue  121 LYS
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  133 ASP
Chi-restraints excluded: chain A residue  176 ILE
Chi-restraints excluded: chain A residue  186 ASN
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  259 ILE
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  290 TYR
Chi-restraints excluded: chain A residue  305 ARG
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  325 PHE
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  489 ASP
Chi-restraints excluded: chain A residue  545 THR
Chi-restraints excluded: chain A residue  570 ASP
Chi-restraints excluded: chain A residue  686 SER
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  750 SER
Chi-restraints excluded: chain A residue  758 VAL
Chi-restraints excluded: chain A residue  776 THR
Chi-restraints excluded: chain A residue  809 ILE
Chi-restraints excluded: chain A residue  812 ILE
Chi-restraints excluded: chain A residue  885 GLU
Chi-restraints excluded: chain A residue  905 SER
Chi-restraints excluded: chain A residue  935 ARG
Chi-restraints excluded: chain A residue  971 LEU
Chi-restraints excluded: chain A residue  972 LYS
Chi-restraints excluded: chain A residue 1049 TYR
Chi-restraints excluded: chain A residue 1155 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 34 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9980
   chunk 101 optimal weight:    8.9990
   chunk 80 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   chunk 110 optimal weight:    0.6980
   chunk 105 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A  76 ASN
** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 941 GLN
** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4595 r_free = 0.4595 target = 0.209293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.171144 restraints weight = 37011.595|
|-----------------------------------------------------------------------------|
r_work (start): 0.4200 rms_B_bonded: 5.55
r_work: 0.3928 rms_B_bonded: 5.20 restraints_weight: 2.0000
r_work (final): 0.3928
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3926
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3926 r_free = 0.3926    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3926 r_free = 0.3926    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3926
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6932
moved from start:          0.7530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   9866  Z= 0.178
  Angle     :  0.796  15.007  13427  Z= 0.408
  Chirality :  0.047   0.343   1479
  Planarity :  0.005   0.073   1632
  Dihedral  : 14.810 168.351   1633
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 17.07
  Ramachandran Plot:
    Outliers :  0.72 %
    Allowed  : 10.96 %
    Favored  : 88.32 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 44.76 %
    Favored  : 51.23 %
  Cbeta Deviations :  0.09 %
  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: -2.22 (0.24), residues: 1115
  helix:  0.01 (0.24), residues: 463
  sheet: -2.81 (0.47), residues: 84
  loop : -2.63 (0.24), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A1071 
 TYR   0.032   0.002   TYR A 903 
 PHE   0.026   0.002   PHE A 490 
 TRP   0.017   0.001   TRP A 890 
 HIS   0.005   0.001   HIS A 502 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 ( 9864)
  covalent geometry    : angle       0.79582 (13427)
  hydrogen bonds       : bond        0.04530 (  357)
  hydrogen bonds       : angle       5.02963 ( 1041)
  Misc. bond           : bond        0.01248 (    2)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 101
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.7099 (pp20)
REVERT: A   61 PHE cc_start: 0.5449 (t80) cc_final: 0.5164 (t80)
REVERT: A  121 LYS cc_start: 0.6477 (OUTLIER) cc_final: 0.5724 (ptpt)
REVERT: A  186 ASN cc_start: 0.4403 (OUTLIER) cc_final: 0.4044 (t0)
REVERT: A  237 TYR cc_start: 0.7218 (t80) cc_final: 0.6490 (t80)
REVERT: A  260 ASN cc_start: 0.7934 (t0) cc_final: 0.7364 (m-40)
REVERT: A  276 LEU cc_start: 0.6695 (OUTLIER) cc_final: 0.6184 (mt)
REVERT: A  325 PHE cc_start: 0.5325 (OUTLIER) cc_final: 0.3608 (m-10)
REVERT: A  552 LYS cc_start: 0.6824 (mppt) cc_final: 0.5999 (mttm)
REVERT: A  686 SER cc_start: 0.5610 (OUTLIER) cc_final: 0.5239 (m)
REVERT: A  691 ASP cc_start: 0.7483 (p0) cc_final: 0.7008 (m-30)
REVERT: A  768 LYS cc_start: 0.6514 (tptp) cc_final: 0.5983 (mttm)
REVERT: A  769 ASN cc_start: 0.6602 (t0) cc_final: 0.6175 (t0)
  outliers start: 37
  outliers final: 26
  residues processed: 132
  average time/residue: 0.4052
  time to fit residues: 58.7984
Evaluate side-chains
  130 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 98
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 GLU
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue  121 LYS
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  133 ASP
Chi-restraints excluded: chain A residue  186 ASN
Chi-restraints excluded: chain A residue  187 MET
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  259 ILE
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  290 TYR
Chi-restraints excluded: chain A residue  305 ARG
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  325 PHE
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  545 THR
Chi-restraints excluded: chain A residue  570 ASP
Chi-restraints excluded: chain A residue  686 SER
Chi-restraints excluded: chain A residue  704 ILE
Chi-restraints excluded: chain A residue  750 SER
Chi-restraints excluded: chain A residue  758 VAL
Chi-restraints excluded: chain A residue  776 THR
Chi-restraints excluded: chain A residue  809 ILE
Chi-restraints excluded: chain A residue  812 ILE
Chi-restraints excluded: chain A residue  905 SER
Chi-restraints excluded: chain A residue  935 ARG
Chi-restraints excluded: chain A residue  971 LEU
Chi-restraints excluded: chain A residue 1049 TYR
Chi-restraints excluded: chain A residue 1155 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 70 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   chunk 80 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 93 optimal weight:    3.9990
   chunk 35 optimal weight:    0.0010
   chunk 101 optimal weight:    0.9990
   chunk 52 optimal weight:    5.9990
   chunk 77 optimal weight:    3.9990
   chunk 65 optimal weight:    0.0970
   overall best weight:    0.5788

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

Flipped N/Q/H residues before XYZ refinement:
A 468 ASN
** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 963 ASN
** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4618 r_free = 0.4618 target = 0.211742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.172927 restraints weight = 39267.224|
|-----------------------------------------------------------------------------|
r_work (start): 0.4220 rms_B_bonded: 5.85
r_work: 0.3956 rms_B_bonded: 5.39 restraints_weight: 2.0000
r_work (final): 0.3956
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3954
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3954 r_free = 0.3954    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3954 r_free = 0.3954    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3954
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6874
moved from start:          0.7787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   9866  Z= 0.160
  Angle     :  0.778  14.791  13427  Z= 0.399
  Chirality :  0.046   0.344   1479
  Planarity :  0.005   0.067   1632
  Dihedral  : 14.785 171.415   1633
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 16.59
  Ramachandran Plot:
    Outliers :  0.72 %
    Allowed  :  9.52 %
    Favored  : 89.76 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 45.38 %
    Favored  : 51.03 %
  Cbeta Deviations :  0.09 %
  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: -2.11 (0.24), residues: 1115
  helix:  0.07 (0.24), residues: 464
  sheet: -2.62 (0.47), residues: 89
  loop : -2.55 (0.25), residues: 562

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A1071 
 TYR   0.027   0.002   TYR A 903 
 PHE   0.018   0.002   PHE A1027 
 TRP   0.018   0.001   TRP A 890 
 HIS   0.004   0.001   HIS A 502 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 9864)
  covalent geometry    : angle       0.77793 (13427)
  hydrogen bonds       : bond        0.04223 (  357)
  hydrogen bonds       : angle       4.89619 ( 1041)
  Misc. bond           : bond        0.01219 (    2)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 108
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.7053 (pp20)
REVERT: A   22 ILE cc_start: 0.6297 (OUTLIER) cc_final: 0.6067 (mp)
REVERT: A   61 PHE cc_start: 0.5552 (t80) cc_final: 0.5297 (t80)
REVERT: A  121 LYS cc_start: 0.6394 (OUTLIER) cc_final: 0.5638 (ptpt)
REVERT: A  186 ASN cc_start: 0.4150 (OUTLIER) cc_final: 0.3857 (t0)
REVERT: A  237 TYR cc_start: 0.7171 (t80) cc_final: 0.6527 (t80)
REVERT: A  260 ASN cc_start: 0.7924 (t0) cc_final: 0.7351 (m-40)
REVERT: A  276 LEU cc_start: 0.6710 (OUTLIER) cc_final: 0.6223 (mt)
REVERT: A  305 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.6812 (tpt90)
REVERT: A  325 PHE cc_start: 0.5265 (OUTLIER) cc_final: 0.3474 (m-10)
REVERT: A  552 LYS cc_start: 0.6751 (mppt) cc_final: 0.5930 (mttm)
REVERT: A  691 ASP cc_start: 0.7359 (p0) cc_final: 0.7015 (m-30)
REVERT: A  768 LYS cc_start: 0.6430 (tptp) cc_final: 0.5890 (mttm)
REVERT: A  769 ASN cc_start: 0.6503 (t0) cc_final: 0.6047 (t0)
  outliers start: 33
  outliers final: 20
  residues processed: 136
  average time/residue: 0.4314
  time to fit residues: 64.2029
Evaluate side-chains
  123 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 96
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 GLU
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue  121 LYS
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  133 ASP
Chi-restraints excluded: chain A residue  186 ASN
Chi-restraints excluded: chain A residue  187 MET
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  276 LEU
Chi-restraints excluded: chain A residue  290 TYR
Chi-restraints excluded: chain A residue  305 ARG
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  325 PHE
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  570 ASP
Chi-restraints excluded: chain A residue  750 SER
Chi-restraints excluded: chain A residue  758 VAL
Chi-restraints excluded: chain A residue  776 THR
Chi-restraints excluded: chain A residue  809 ILE
Chi-restraints excluded: chain A residue  812 ILE
Chi-restraints excluded: chain A residue  905 SER
Chi-restraints excluded: chain A residue  935 ARG
Chi-restraints excluded: chain A residue  971 LEU
Chi-restraints excluded: chain A residue 1049 TYR
Chi-restraints excluded: chain A residue 1155 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 58 optimal weight:    5.9990
   chunk 43 optimal weight:    4.9990
   chunk 55 optimal weight:    0.5980
   chunk 25 optimal weight:   10.0000
   chunk 60 optimal weight:    0.7980
   chunk 86 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9990
   chunk 107 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 30 optimal weight:    0.1980
   chunk 85 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4638 r_free = 0.4638 target = 0.212336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.173861 restraints weight = 34776.465|
|-----------------------------------------------------------------------------|
r_work (start): 0.4239 rms_B_bonded: 5.30
r_work: 0.3991 rms_B_bonded: 5.10 restraints_weight: 2.0000
r_work (final): 0.3991
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3990
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3990 r_free = 0.3990    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3990 r_free = 0.3990    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3990
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6896
moved from start:          0.7871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   9866  Z= 0.164
  Angle     :  0.780  14.758  13427  Z= 0.400
  Chirality :  0.046   0.340   1479
  Planarity :  0.005   0.058   1632
  Dihedral  : 14.742 170.618   1633
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 16.11
  Ramachandran Plot:
    Outliers :  0.72 %
    Allowed  : 10.33 %
    Favored  : 88.95 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 45.48 %
    Favored  : 50.92 %
  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: -2.06 (0.24), residues: 1115
  helix:  0.10 (0.24), residues: 464
  sheet: -2.57 (0.47), residues: 89
  loop : -2.52 (0.25), residues: 562

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A1071 
 TYR   0.030   0.002   TYR A 903 
 PHE   0.024   0.002   PHE A 490 
 TRP   0.016   0.001   TRP A 890 
 HIS   0.004   0.001   HIS A 502 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 9864)
  covalent geometry    : angle       0.78042 (13427)
  hydrogen bonds       : bond        0.04241 (  357)
  hydrogen bonds       : angle       4.90047 ( 1041)
  Misc. bond           : bond        0.01217 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4157.85 seconds
wall clock time: 71 minutes 39.59 seconds (4299.59 seconds total)