Starting phenix.real_space_refine
on Wed Jul 30 15:33:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6kl9_0704/07_2025/6kl9_0704_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6kl9_0704/07_2025/6kl9_0704.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.25
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6kl9_0704/07_2025/6kl9_0704.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6kl9_0704/07_2025/6kl9_0704.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6kl9_0704/07_2025/6kl9_0704_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6kl9_0704/07_2025/6kl9_0704_neut.cif"
  }
  resolution = 3.25
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P      25      5.49       5
     Mg      2      5.21       5
     S      39      5.16       5
     C    7722      2.51       5
     N    2005      2.21       5
     O    2398      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12191
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 9720
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1180, 9711
          Classifications: {'peptide': 1180}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 24, 'TRANS': 1155}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 16
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
      Conformer: "B"
        Number of residues, atoms: 1180, 9711
          Classifications: {'peptide': 1180}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 24, 'TRANS': 1155}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 16
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
          bond proxies already assigned to first conformer: 9895
    Chain: "B"
      Number of atoms: 967
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 967
          Classifications: {'peptide': 117}
          Link IDs: {'PTRANS': 7, 'TRANS': 109}
    Chain: "C"
      Number of atoms: 967
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 967
          Classifications: {'peptide': 117}
          Link IDs: {'PTRANS': 7, 'TRANS': 109}
    Chain: "G"
      Number of atoms: 529
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 529
          Classifications: {'RNA': 25}
          Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 7, 'rna3p_pyr': 9}
          Link IDs: {'rna2p': 9, 'rna3p': 15}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "G"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 7
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1, 'water': 6}
          Link IDs: {None: 6}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ALYS A 775 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NZ BLYS A 775 " occ=0.50
  Time building chain proxies: 12.37, per 1000 atoms: 1.01
  Number of scatterers: 12191
  At special positions: 0
  Unit cell: (124.2, 125.28, 128.52, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      39     16.00
     P      25     15.00
     Mg      2     11.99
     O    2398      8.00
     N    2005      7.00
     C    7722      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 131 " - pdb=" SG  CYS C 131 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.03
  Conformation dependent library (CDL) restraints added in 2.5 seconds
  

  2798 Ramachandran restraints generated.
    1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2712

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 15 sheets defined
      46.3% alpha, 10.5% beta
      4 base pairs and 11 stacking pairs defined.
    Time for finding SS restraints: 3.95
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 7
      removed outlier: 3.700A  pdb=" N   LYS A   6 " --> pdb=" O   LYS A   3 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 26 through 35
    Processing helix  chain 'A' and resid 40 through 46
    Processing helix  chain 'A' and resid 46 through 66
      removed outlier: 3.762A  pdb=" N   VAL A  50 " --> pdb=" O   ASP A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 69
      No H-bonds generated for 'chain 'A' and resid 67 through 69'
    Processing helix  chain 'A' and resid 73 through 80
      removed outlier: 3.539A  pdb=" N   TYR A  77 " --> pdb=" O   ASN A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 112
      removed outlier: 4.446A  pdb=" N   ASN A 112 " --> pdb=" O   ALA A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 125
      removed outlier: 3.680A  pdb=" N   ILE A 123 " --> pdb=" O   LYS A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 132
    Processing helix  chain 'A' and resid 134 through 143
    Processing helix  chain 'A' and resid 151 through 159
    Processing helix  chain 'A' and resid 171 through 176
    Processing helix  chain 'A' and resid 178 through 194
      removed outlier: 4.108A  pdb=" N   ARG A 182 " --> pdb=" O   GLU A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 211
      removed outlier: 3.508A  pdb=" N   LYS A 208 " --> pdb=" O   GLU A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 221
      removed outlier: 3.679A  pdb=" N   GLU A 221 " --> pdb=" O   ASP A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 229
    Processing helix  chain 'A' and resid 230 through 242
      removed outlier: 3.895A  pdb=" N   ILE A 234 " --> pdb=" O   THR A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 263
      removed outlier: 4.422A  pdb=" N   ASN A 263 " --> pdb=" O   ILE A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 309
      removed outlier: 3.641A  pdb=" N   LEU A 301 " --> pdb=" O   ASP A 297 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   LEU A 308 " --> pdb=" O   PHE A 304 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ASN A 309 " --> pdb=" O   ARG A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 325
    Processing helix  chain 'A' and resid 342 through 350
      removed outlier: 3.890A  pdb=" N   THR A 346 " --> pdb=" O   PRO A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 371
      removed outlier: 3.921A  pdb=" N   ILE A 369 " --> pdb=" O   GLU A 365 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   LEU A 371 " --> pdb=" O   ASP A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 392
      removed outlier: 3.643A  pdb=" N   GLU A 382 " --> pdb=" O   THR A 378 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   ILE A 392 " --> pdb=" O   SER A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 402
    Processing helix  chain 'A' and resid 409 through 432
    Processing helix  chain 'A' and resid 449 through 472
      removed outlier: 3.615A  pdb=" N   VAL A 453 " --> pdb=" O   ASN A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 488
    Processing helix  chain 'A' and resid 493 through 512
      removed outlier: 4.109A  pdb=" N   LEU A 497 " --> pdb=" O   ALA A 493 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   THR A 512 " --> pdb=" O   ARG A 508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 563 through 567
      removed outlier: 3.831A  pdb=" N   GLN A 567 " --> pdb=" O   LYS A 564 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 588 through 591
      removed outlier: 4.342A  pdb=" N   LYS A 591 " --> pdb=" O   GLY A 588 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 588 through 591'
    Processing helix  chain 'A' and resid 592 through 598
      removed outlier: 4.034A  pdb=" N   VAL A 596 " --> pdb=" O   MET A 592 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   PHE A 597 " --> pdb=" O   LEU A 593 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 612 through 619
    Processing helix  chain 'A' and resid 629 through 642
    Processing helix  chain 'A' and resid 666 through 676
    Processing helix  chain 'A' and resid 686 through 697
      removed outlier: 4.052A  pdb=" N   VAL A 690 " --> pdb=" O   SER A 686 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 706 through 710
    Processing helix  chain 'A' and resid 718 through 726
      removed outlier: 3.699A  pdb=" N   MET A 722 " --> pdb=" O   ASN A 718 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 752 through 756
      removed outlier: 3.874A  pdb=" N   LEU A 756 " --> pdb=" O   LYS A 753 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 786 through 790
      removed outlier: 3.648A  pdb=" N   PHE A 789 " --> pdb=" O   ASP A 786 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   SER A 790 " --> pdb=" O   LYS A 787 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 786 through 790'
    Processing helix  chain 'A' and resid 811 through 822
      removed outlier: 3.573A  pdb=" N   GLU A 815 " --> pdb=" O   LYS A 811 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 872 through 885
      removed outlier: 3.795A  pdb=" N   GLU A 885 " --> pdb=" O   LYS A 881 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 890 through 919
      removed outlier: 3.852A  pdb=" N   GLU A 894 " --> pdb=" O   TRP A 890 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 939 through 954
    Processing helix  chain 'A' and resid 1021 through 1031
    Processing helix  chain 'A' and resid 1091 through 1100
    Processing helix  chain 'A' and resid 1101 through 1104
      removed outlier: 4.180A  pdb=" N   ILE A1104 " --> pdb=" O   LYS A1101 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1101 through 1104'
    Processing helix  chain 'A' and resid 1111 through 1116
    Processing helix  chain 'A' and resid 1120 through 1135
      removed outlier: 4.478A  pdb=" N   TYR A1124 " --> pdb=" O   ASP A1120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1163 through 1167
    Processing helix  chain 'A' and resid 1178 through 1199
      removed outlier: 3.612A  pdb=" N   ASN A1182 " --> pdb=" O   ASN A1178 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLY A1183 " --> pdb=" O   ALA A1179 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   LYS A1199 " --> pdb=" O   ILE A1195 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1205 through 1209
      removed outlier: 3.646A  pdb=" N   VAL A1209 " --> pdb=" O   LEU A1206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1214 through 1225
    Processing helix  chain 'B' and resid 118 through 149
      removed outlier: 3.869A  pdb=" N   LEU B 122 " --> pdb=" O   ASP B 118 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 228 through 232
      removed outlier: 3.506A  pdb=" N   LEU B 232 " --> pdb=" O   VAL B 229 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 118 through 150
      removed outlier: 4.026A  pdb=" N   LEU C 122 " --> pdb=" O   ASP C 118 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 166 through 170
      removed outlier: 3.754A  pdb=" N   LEU C 170 " --> pdb=" O   PRO C 167 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 200 through 204
      removed outlier: 3.827A  pdb=" N   ARG C 203 " --> pdb=" O   SER C 200 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   GLU C 204 " --> pdb=" O   THR C 201 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 200 through 204'
    Processing helix  chain 'C' and resid 228 through 232
      removed outlier: 3.586A  pdb=" N   LEU C 232 " --> pdb=" O   VAL C 229 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 520 through 522
      removed outlier: 3.688A  pdb=" N   PHE A 521 " --> pdb=" O   MET A 746 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   LYS A  20 " --> pdb=" O   TYR A 705 " (cutoff:3.500A)
      removed outlier: 6.191A  pdb=" N   ILE A 546 " --> pdb=" O   ILE A 581 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 520 through 522
      removed outlier: 3.688A  pdb=" N   PHE A 521 " --> pdb=" O   MET A 746 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 243 through 244
      removed outlier: 3.814A  pdb=" N   PHE A 244 " --> pdb=" O   ILE A 252 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ILE A 252 " --> pdb=" O   PHE A 244 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 337 through 338
    Processing sheet with id=AA5, first strand: chain 'A' and resid 758 through 759
    Processing sheet with id=AA6, first strand: chain 'A' and resid 765 through 766
    Processing sheet with id=AA7, first strand: chain 'A' and resid 850 through 855
    Processing sheet with id=AA8, first strand: chain 'A' and resid 858 through 863
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1033 through 1037
      removed outlier: 3.627A  pdb=" N   ALA A1046 " --> pdb=" O   ARG A1033 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1070 through 1073
    Processing sheet with id=AB2, first strand: chain 'A' and resid 1138 through 1140
    Processing sheet with id=AB3, first strand: chain 'B' and resid 180 through 181
      removed outlier: 3.788A  pdb=" N   GLU B 180 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 183 through 187
      removed outlier: 4.917A  pdb=" N   CYS B 185 " --> pdb=" O   CYS B 195 " (cutoff:3.500A)
      removed outlier: 7.202A  pdb=" N   CYS B 195 " --> pdb=" O   CYS B 185 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 158 through 161
    Processing sheet with id=AB6, first strand: chain 'C' and resid 183 through 187
      removed outlier: 3.502A  pdb=" N   TYR C 197 " --> pdb=" O   GLY C 183 " (cutoff:3.500A)
      removed outlier: 5.237A  pdb=" N   CYS C 185 " --> pdb=" O   CYS C 195 " (cutoff:3.500A)
      removed outlier: 7.615A  pdb=" N   CYS C 195 " --> pdb=" O   CYS C 185 " (cutoff:3.500A)

    494 hydrogen bonds defined for protein.
    1365 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      9 hydrogen bonds
      14 hydrogen bond angles
      0 basepair planarities
      4 basepair parallelities
      11 stacking parallelities
  Total time for adding SS restraints: 4.89

  Time building geometry restraints manager: 3.63 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 3559
        1.34 -     1.46: 3047
        1.46 -     1.58: 5760
        1.58 -     1.71: 48
        1.71 -     1.83: 63
  Bond restraints: 12477
  Sorted by residual:
  bond pdb=" C   LEU A 128 "
       pdb=" N   PRO A 129 "
    ideal  model  delta    sigma   weight residual
    1.336  1.363 -0.027 1.20e-02 6.94e+03 5.14e+00
  bond pdb=" CA  VAL B 216 "
       pdb=" C   VAL B 216 "
    ideal  model  delta    sigma   weight residual
    1.523  1.547 -0.024 1.27e-02 6.20e+03 3.71e+00
  bond pdb=" N   ARG B 187 "
       pdb=" CA  ARG B 187 "
    ideal  model  delta    sigma   weight residual
    1.454  1.476 -0.021 1.15e-02 7.56e+03 3.48e+00
  bond pdb=" C   GLY A 588 "
       pdb=" N   PRO A 589 "
    ideal  model  delta    sigma   weight residual
    1.331  1.346 -0.015 7.90e-03 1.60e+04 3.40e+00
  bond pdb=" C   TYR B 144 "
       pdb=" O   TYR B 144 "
    ideal  model  delta    sigma   weight residual
    1.237  1.217  0.020 1.19e-02 7.06e+03 2.74e+00
  ... (remaining 12472 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.84: 16530
        2.84 -     5.69: 318
        5.69 -     8.53: 52
        8.53 -    11.37: 12
       11.37 -    14.22: 1
  Bond angle restraints: 16913
  Sorted by residual:
  angle pdb=" N   PHE A 131 "
        pdb=" CA  PHE A 131 "
        pdb=" C   PHE A 131 "
      ideal   model   delta    sigma   weight residual
     111.03  121.19  -10.16 1.11e+00 8.12e-01 8.38e+01
  angle pdb=" N   ASP A 450 "
        pdb=" CA  ASP A 450 "
        pdb=" C   ASP A 450 "
      ideal   model   delta    sigma   weight residual
     111.28  120.45   -9.17 1.09e+00 8.42e-01 7.07e+01
  angle pdb=" N   LEU A1047 "
        pdb=" CA  LEU A1047 "
        pdb=" C   LEU A1047 "
      ideal   model   delta    sigma   weight residual
     108.48  122.70  -14.22 1.80e+00 3.09e-01 6.24e+01
  angle pdb=" N   VAL A 758 "
        pdb=" CA  VAL A 758 "
        pdb=" C   VAL A 758 "
      ideal   model   delta    sigma   weight residual
     108.27  118.12   -9.85 1.37e+00 5.33e-01 5.17e+01
  angle pdb=" N   HIS C 190 "
        pdb=" CA  HIS C 190 "
        pdb=" C   HIS C 190 "
      ideal   model   delta    sigma   weight residual
     114.75  106.59    8.16 1.26e+00 6.30e-01 4.20e+01
  ... (remaining 16908 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.95: 7475
       35.95 -    71.90: 125
       71.90 -   107.86: 9
      107.86 -   143.81: 2
      143.81 -   179.76: 3
  Dihedral angle restraints: 7614
    sinusoidal: 3412
      harmonic: 4202
  Sorted by residual:
  dihedral pdb=" O4'   C G  21 "
           pdb=" C1'   C G  21 "
           pdb=" N1    C G  21 "
           pdb=" C2    C G  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   51.76 -179.76     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" O4'   U G  14 "
           pdb=" C1'   U G  14 "
           pdb=" N1    U G  14 "
           pdb=" C2    U G  14 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   50.39 -178.39     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" CB  CYS B 131 "
           pdb=" SG  CYS B 131 "
           pdb=" SG  CYS C 131 "
           pdb=" CB  CYS C 131 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -141.09   55.09     1      1.00e+01 1.00e-02 4.11e+01
  ... (remaining 7611 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.099: 1685
       0.099 -    0.198: 134
       0.198 -    0.298: 20
       0.298 -    0.397: 4
       0.397 -    0.496: 2
  Chirality restraints: 1845
  Sorted by residual:
  chirality pdb=" CA  ASN A 928 "
            pdb=" N   ASN A 928 "
            pdb=" C   ASN A 928 "
            pdb=" CB  ASN A 928 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.01    0.50 2.00e-01 2.50e+01 6.15e+00
  chirality pdb=" CA  LEU A1047 "
            pdb=" N   LEU A1047 "
            pdb=" C   LEU A1047 "
            pdb=" CB  LEU A1047 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 4.00e+00
  chirality pdb=" CB  VAL A 228 "
            pdb=" CA  VAL A 228 "
            pdb=" CG1 VAL A 228 "
            pdb=" CG2 VAL A 228 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.28   -0.35 2.00e-01 2.50e+01 3.03e+00
  ... (remaining 1842 not shown)

  Planarity restraints: 2077
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 991 "   -0.018 2.00e-02 2.50e+03   3.61e-02 1.30e+01
        pdb=" C   GLY A 991 "    0.062 2.00e-02 2.50e+03
        pdb=" O   GLY A 991 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   PHE A 992 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS A 720 "    0.021 2.00e-02 2.50e+03   2.58e-02 9.98e+00
        pdb=" CG  HIS A 720 "   -0.055 2.00e-02 2.50e+03
        pdb=" ND1 HIS A 720 "    0.016 2.00e-02 2.50e+03
        pdb=" CD2 HIS A 720 "    0.015 2.00e-02 2.50e+03
        pdb=" CE1 HIS A 720 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE2 HIS A 720 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 527 "   -0.050 5.00e-02 4.00e+02   7.67e-02 9.42e+00
        pdb=" N   PRO A 528 "    0.133 5.00e-02 4.00e+02
        pdb=" CA  PRO A 528 "   -0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO A 528 "   -0.042 5.00e-02 4.00e+02
  ... (remaining 2074 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 96
        2.60 -     3.18: 9696
        3.18 -     3.75: 17176
        3.75 -     4.33: 24374
        4.33 -     4.90: 39653
  Nonbonded interactions: 90995
  Sorted by model distance:
  nonbonded pdb="MG    MG G 101 "
            pdb=" O   HOH G 202 "
     model   vdw
     2.031 2.170
  nonbonded pdb="MG    MG G 101 "
            pdb=" O   HOH G 205 "
     model   vdw
     2.035 2.170
  nonbonded pdb="MG    MG G 101 "
            pdb=" O   HOH G 204 "
     model   vdw
     2.036 2.170
  nonbonded pdb="MG    MG G 101 "
            pdb=" O   HOH G 206 "
     model   vdw
     2.045 2.170
  nonbonded pdb="MG    MG G 101 "
            pdb=" O   HOH G 201 "
     model   vdw
     2.046 2.170
  ... (remaining 90990 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
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
}

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=0.50 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:             14.930
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.460
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     40.400
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.090
  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:3.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   59.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7250
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      :  0.005   0.051  12478  Z= 0.248
  Angle     :  1.009  14.216  16915  Z= 0.607
  Chirality :  0.063   0.496   1845
  Planarity :  0.007   0.077   2077
  Dihedral  : 13.562 179.759   4899
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  9.74 %
    Favored  : 90.04 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  :  2.95 %
    Favored  : 94.33 %
  Cbeta Deviations :  0.07 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.82 (0.16), residues: 1399
  helix: -3.28 (0.13), residues: 585
  sheet: -0.77 (0.57), residues: 87
  loop : -3.52 (0.18), residues: 727

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.003   TRP A1218 
 HIS   0.031   0.002   HIS A 720 
 PHE   0.027   0.002   PHE A 474 
 TYR   0.027   0.002   TYR A1049 
 ARG   0.009   0.001   ARG A 543 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16885 (  496)
  hydrogen bonds       : angle       9.14442 ( 1379)
  SS BOND              : bond        0.00059 (    1)
  SS BOND              : angle       2.44960 (    2)
  covalent geometry    : bond        0.00458 (12477)
  covalent geometry    : angle       1.00908 (16913)

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

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

  2798 Ramachandran restraints generated.
    1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2798 Ramachandran restraints generated.
    1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  376 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 342
  time to evaluate  : 1.441 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 HIS cc_start: 0.7748 (t70) cc_final: 0.7458 (t-90)
REVERT: A  107 LYS cc_start: 0.8050 (tptm) cc_final: 0.7436 (tttm)
REVERT: A  135 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7582 (mmtt)
REVERT: A  179 ASN cc_start: 0.7659 (m-40) cc_final: 0.7434 (m-40)
REVERT: A  278 LYS cc_start: 0.7699 (mppt) cc_final: 0.7007 (pttp)
REVERT: A  875 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8131 (tp)
REVERT: A  878 LYS cc_start: 0.7812 (mtmt) cc_final: 0.7477 (tttt)
REVERT: A  925 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8091 (pp20)
REVERT: A 1003 LYS cc_start: 0.8200 (mtmp) cc_final: 0.7870 (mtpt)
REVERT: A 1112 ARG cc_start: 0.5316 (OUTLIER) cc_final: 0.4992 (ttp-170)
REVERT: A 1131 MET cc_start: 0.7577 (mmm) cc_final: 0.7312 (mmt)
REVERT: A 1133 LEU cc_start: 0.8255 (mp) cc_final: 0.7973 (tp)
REVERT: A 1134 MET cc_start: 0.7236 (ttp) cc_final: 0.6944 (ttp)
REVERT: A 1137 MET cc_start: 0.7040 (ttm) cc_final: 0.6830 (mtp)
REVERT: A 1204 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7448 (mm-30)
REVERT: B  132 ILE cc_start: 0.8202 (mt) cc_final: 0.7995 (mt)
REVERT: B  134 LYS cc_start: 0.7596 (mttm) cc_final: 0.6961 (mttt)
REVERT: B  158 VAL cc_start: 0.8604 (t) cc_final: 0.8127 (m)
REVERT: B  166 ASP cc_start: 0.7154 (OUTLIER) cc_final: 0.6827 (p0)
REVERT: B  169 ASN cc_start: 0.7894 (t0) cc_final: 0.7569 (t0)
REVERT: B  188 TYR cc_start: 0.8607 (OUTLIER) cc_final: 0.7926 (t80)
REVERT: B  209 TYR cc_start: 0.8462 (m-80) cc_final: 0.8129 (m-10)
REVERT: B  217 ARG cc_start: 0.7799 (ptt-90) cc_final: 0.7515 (ptt-90)
REVERT: B  222 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.7149 (mtm-85)
  outliers start: 34
  outliers final: 22
  residues processed: 371
  average time/residue: 0.2868
  time to fit residues: 146.7845
Evaluate side-chains
  226 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 197
  time to evaluate  : 1.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 GLU
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  136 ASP
Chi-restraints excluded: chain A residue  450 ASP
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  592 MET
Chi-restraints excluded: chain A residue  756 LEU
Chi-restraints excluded: chain A residue  875 LEU
Chi-restraints excluded: chain A residue  888 GLN
Chi-restraints excluded: chain A residue  889 ASN
Chi-restraints excluded: chain A residue  891 THR
Chi-restraints excluded: chain A residue  922 ILE
Chi-restraints excluded: chain A residue  924 LEU
Chi-restraints excluded: chain A residue  925 GLU
Chi-restraints excluded: chain A residue  926 ASP
Chi-restraints excluded: chain A residue  927 LEU
Chi-restraints excluded: chain A residue  996 ILE
Chi-restraints excluded: chain A residue 1001 THR
Chi-restraints excluded: chain A residue 1033 ARG
Chi-restraints excluded: chain A residue 1035 MET
Chi-restraints excluded: chain A residue 1047 LEU
Chi-restraints excluded: chain A residue 1112 ARG
Chi-restraints excluded: chain A residue 1187 ILE
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain B residue  166 ASP
Chi-restraints excluded: chain B residue  188 TYR
Chi-restraints excluded: chain B residue  190 HIS
Chi-restraints excluded: chain B residue  192 ASP
Chi-restraints excluded: chain B residue  222 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 119 optimal weight:    0.0870
   chunk 107 optimal weight:    7.9990
   chunk 59 optimal weight:    7.9990
   chunk 36 optimal weight:   10.0000
   chunk 72 optimal weight:    0.7980
   chunk 57 optimal weight:    0.4980
   chunk 111 optimal weight:    0.8980
   chunk 43 optimal weight:    0.0770
   chunk 67 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 128 optimal weight:    2.9990
   overall best weight:    0.4716

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

Flipped N/Q/H residues before XYZ refinement:
A 226 ASN
A 268 GLN
A 577 ASN
A 582 ASN
A 803 ASN
A 813 ASN
A 955 ASN
A 963 ASN
A 989 GLN
A1012 ASN
A1051 ASN
** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.210263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.178469 restraints weight = 24285.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.4056 rms_B_bonded: 3.87
r_work (final): 0.4056
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4056
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4056 r_free = 0.4056    target_work(ls_wunit_k1) = 0.177         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4056 r_free = 0.4056    target_work(ls_wunit_k1) = 0.177         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4056
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7056
moved from start:          0.2507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  12478  Z= 0.135
  Angle     :  0.637   8.950  16915  Z= 0.345
  Chirality :  0.044   0.253   1845
  Planarity :  0.005   0.060   2077
  Dihedral  : 14.984 177.513   1991
  Min Nonbonded Distance : 1.876

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  8.09 %
    Favored  : 91.76 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 10.49 %
    Favored  : 87.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.93 (0.20), residues: 1399
  helix: -0.89 (0.19), residues: 583
  sheet: -1.44 (0.45), residues: 128
  loop : -3.08 (0.20), residues: 688

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A1218 
 HIS   0.012   0.001   HIS A 720 
 PHE   0.031   0.001   PHE A 173 
 TYR   0.021   0.002   TYR A1036 
 ARG   0.004   0.001   ARG A  43 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05554 (  496)
  hydrogen bonds       : angle       5.55545 ( 1379)
  SS BOND              : bond        0.01004 (    1)
  SS BOND              : angle       5.54063 (    2)
  covalent geometry    : bond        0.00281 (12477)
  covalent geometry    : angle       0.63386 (16913)

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

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

  2798 Ramachandran restraints generated.
    1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2798 Ramachandran restraints generated.
    1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 220
  time to evaluate  : 1.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 LYS cc_start: 0.8067 (tptm) cc_final: 0.7783 (tttt)
REVERT: A  268 GLN cc_start: 0.5382 (mm-40) cc_final: 0.5032 (mm-40)
REVERT: A  481 ASN cc_start: 0.7097 (p0) cc_final: 0.6891 (p0)
REVERT: A  765 ILE cc_start: 0.6654 (pt) cc_final: 0.6255 (tp)
REVERT: A  824 ASP cc_start: 0.8007 (p0) cc_final: 0.7802 (p0)
REVERT: A  875 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8279 (tp)
REVERT: A 1133 LEU cc_start: 0.8287 (mp) cc_final: 0.8009 (tt)
REVERT: A 1137 MET cc_start: 0.7190 (ttm) cc_final: 0.6983 (mtp)
REVERT: B  169 ASN cc_start: 0.7081 (t0) cc_final: 0.6832 (t0)
REVERT: B  188 TYR cc_start: 0.8366 (OUTLIER) cc_final: 0.8118 (t80)
  outliers start: 30
  outliers final: 14
  residues processed: 241
  average time/residue: 0.2321
  time to fit residues: 81.6910
Evaluate side-chains
  188 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 172
  time to evaluate  : 1.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 ASP
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  431 SER
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  450 ASP
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  552 LYS
Chi-restraints excluded: chain A residue  844 VAL
Chi-restraints excluded: chain A residue  875 LEU
Chi-restraints excluded: chain A residue  927 LEU
Chi-restraints excluded: chain A residue 1047 LEU
Chi-restraints excluded: chain A residue 1051 ASN
Chi-restraints excluded: chain B residue  188 TYR
Chi-restraints excluded: chain B residue  192 ASP
Chi-restraints excluded: chain C residue  225 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 141 optimal weight:    2.9990
   chunk 98 optimal weight:    4.9990
   chunk 78 optimal weight:    4.9990
   chunk 15 optimal weight:    2.9990
   chunk 112 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 26 optimal weight:    6.9990
   chunk 56 optimal weight:    3.9990
   chunk 36 optimal weight:   10.0000
   chunk 87 optimal weight:    0.5980
   overall best weight:    2.3188

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

Flipped N/Q/H residues before XYZ refinement:
A 100 ASN
A 797 HIS
B 145 ASN
C 231 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.197812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.163551 restraints weight = 25183.793|
|-----------------------------------------------------------------------------|
r_work (start): 0.3910 rms_B_bonded: 3.93
r_work (final): 0.3910
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3910
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3910 r_free = 0.3910    target_work(ls_wunit_k1) = 0.163         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3910 r_free = 0.3910    target_work(ls_wunit_k1) = 0.163         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3910
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7316
moved from start:          0.3395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.076  12478  Z= 0.282
  Angle     :  0.774   7.945  16915  Z= 0.417
  Chirality :  0.050   0.261   1845
  Planarity :  0.005   0.056   2077
  Dihedral  : 14.498 174.718   1938
  Min Nonbonded Distance : 1.802

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  9.96 %
    Favored  : 89.90 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 11.03 %
    Favored  : 85.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.50 (0.20), residues: 1399
  helix: -0.23 (0.20), residues: 588
  sheet: -1.79 (0.41), residues: 136
  loop : -3.05 (0.20), residues: 675

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.003   TRP A1218 
 HIS   0.028   0.003   HIS A 720 
 PHE   0.056   0.003   PHE A1027 
 TYR   0.029   0.003   TYR A1185 
 ARG   0.008   0.001   ARG B 155 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08308 (  496)
  hydrogen bonds       : angle       5.71656 ( 1379)
  SS BOND              : bond        0.01415 (    1)
  SS BOND              : angle       5.44986 (    2)
  covalent geometry    : bond        0.00654 (12477)
  covalent geometry    : angle       0.77156 (16913)

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

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

  2798 Ramachandran restraints generated.
    1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2798 Ramachandran restraints generated.
    1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 202
  time to evaluate  : 1.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 ILE cc_start: 0.7846 (OUTLIER) cc_final: 0.7557 (mt)
REVERT: A  107 LYS cc_start: 0.8264 (tptm) cc_final: 0.7964 (ttpt)
REVERT: A  231 GLN cc_start: 0.6941 (tp40) cc_final: 0.6684 (tp40)
REVERT: A  875 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8361 (tp)
REVERT: A 1137 MET cc_start: 0.7191 (ttm) cc_final: 0.6986 (mtp)
REVERT: B  188 TYR cc_start: 0.8663 (OUTLIER) cc_final: 0.8440 (t80)
REVERT: C  134 LYS cc_start: 0.7117 (mttm) cc_final: 0.6897 (mtpp)
  outliers start: 49
  outliers final: 37
  residues processed: 236
  average time/residue: 0.2378
  time to fit residues: 81.9554
Evaluate side-chains
  215 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 175
  time to evaluate  : 1.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   67 HIS
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  136 ASP
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  312 SER
Chi-restraints excluded: chain A residue  319 LYS
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain A residue  418 ILE
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  431 SER
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  450 ASP
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  552 LYS
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain A residue  757 VAL
Chi-restraints excluded: chain A residue  802 ILE
Chi-restraints excluded: chain A residue  809 ILE
Chi-restraints excluded: chain A residue  810 PHE
Chi-restraints excluded: chain A residue  844 VAL
Chi-restraints excluded: chain A residue  868 ILE
Chi-restraints excluded: chain A residue  875 LEU
Chi-restraints excluded: chain A residue  888 GLN
Chi-restraints excluded: chain A residue  927 LEU
Chi-restraints excluded: chain A residue 1014 LEU
Chi-restraints excluded: chain B residue  121 TYR
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  188 TYR
Chi-restraints excluded: chain B residue  192 ASP
Chi-restraints excluded: chain B residue  220 ILE
Chi-restraints excluded: chain B residue  229 VAL
Chi-restraints excluded: chain C residue  137 ASP
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  220 ILE
Chi-restraints excluded: chain C residue  225 THR
Chi-restraints excluded: chain C residue  228 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 34 optimal weight:    0.4980
   chunk 36 optimal weight:   10.0000
   chunk 72 optimal weight:    2.9990
   chunk 55 optimal weight:    0.0980
   chunk 20 optimal weight:    0.7980
   chunk 65 optimal weight:    0.6980
   chunk 47 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9980
   chunk 140 optimal weight:    0.9990
   chunk 135 optimal weight:   10.0000
   chunk 128 optimal weight:    2.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 142 ASN
A 279 GLN
A 793 GLN
A 888 GLN
B 145 ASN
C 145 ASN
C 193 GLN
C 231 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.204892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.179715 restraints weight = 16498.248|
|-----------------------------------------------------------------------------|
r_work (start): 0.4080 rms_B_bonded: 2.02
r_work: 0.3569 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3545
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3545 r_free = 0.3545    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3545 r_free = 0.3545    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3545
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.3640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  12478  Z= 0.137
  Angle     :  0.607   8.625  16915  Z= 0.330
  Chirality :  0.043   0.210   1845
  Planarity :  0.004   0.048   2077
  Dihedral  : 14.108 179.474   1936
  Min Nonbonded Distance : 1.883

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  8.31 %
    Favored  : 91.55 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 13.13 %
    Favored  : 84.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.75 (0.21), residues: 1399
  helix:  0.58 (0.21), residues: 580
  sheet: -1.38 (0.44), residues: 129
  loop : -2.78 (0.21), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A1086 
 HIS   0.010   0.001   HIS A 720 
 PHE   0.050   0.001   PHE A1027 
 TYR   0.017   0.001   TYR A 237 
 ARG   0.006   0.000   ARG A 867 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05518 (  496)
  hydrogen bonds       : angle       5.04130 ( 1379)
  SS BOND              : bond        0.00936 (    1)
  SS BOND              : angle       4.01265 (    2)
  covalent geometry    : bond        0.00294 (12477)
  covalent geometry    : angle       0.60539 (16913)

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

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

  2798 Ramachandran restraints generated.
    1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2798 Ramachandran restraints generated.
    1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 196
  time to evaluate  : 1.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 ILE cc_start: 0.7720 (OUTLIER) cc_final: 0.7493 (mt)
REVERT: A  107 LYS cc_start: 0.8147 (tptm) cc_final: 0.7740 (ttpt)
REVERT: A  426 TYR cc_start: 0.7009 (OUTLIER) cc_final: 0.5221 (t80)
REVERT: A  471 LYS cc_start: 0.8106 (tmmt) cc_final: 0.7761 (tttp)
REVERT: A  875 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8367 (tp)
REVERT: A 1066 TYR cc_start: 0.8122 (m-10) cc_final: 0.7908 (m-10)
REVERT: A 1133 LEU cc_start: 0.8404 (mp) cc_final: 0.8201 (tp)
REVERT: A 1137 MET cc_start: 0.7743 (ttm) cc_final: 0.7131 (mtp)
REVERT: B  211 VAL cc_start: 0.7824 (OUTLIER) cc_final: 0.7588 (t)
REVERT: C  186 MET cc_start: 0.6859 (ptp) cc_final: 0.6559 (pmm)
  outliers start: 34
  outliers final: 23
  residues processed: 218
  average time/residue: 0.2359
  time to fit residues: 77.2892
Evaluate side-chains
  202 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 175
  time to evaluate  : 1.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  377 VAL
Chi-restraints excluded: chain A residue  418 ILE
Chi-restraints excluded: chain A residue  426 TYR
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  450 ASP
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  552 LYS
Chi-restraints excluded: chain A residue  757 VAL
Chi-restraints excluded: chain A residue  802 ILE
Chi-restraints excluded: chain A residue  809 ILE
Chi-restraints excluded: chain A residue  875 LEU
Chi-restraints excluded: chain A residue  889 ASN
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  190 HIS
Chi-restraints excluded: chain B residue  192 ASP
Chi-restraints excluded: chain B residue  211 VAL
Chi-restraints excluded: chain B residue  220 ILE
Chi-restraints excluded: chain B residue  229 VAL
Chi-restraints excluded: chain C residue  131 CYS
Chi-restraints excluded: chain C residue  137 ASP
Chi-restraints excluded: chain C residue  225 THR
Chi-restraints excluded: chain C residue  228 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 102 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 116 optimal weight:    4.9990
   chunk 90 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 10 optimal weight:    8.9990
   chunk 72 optimal weight:    1.9990
   chunk 62 optimal weight:   10.0000
   chunk 71 optimal weight:    0.6980
   chunk 12 optimal weight:    0.7980
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A  67 HIS
A 231 GLN
A 793 GLN
C 231 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.202589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.168761 restraints weight = 27294.481|
|-----------------------------------------------------------------------------|
r_work (start): 0.3962 rms_B_bonded: 4.09
r_work (final): 0.3962
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3962
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3962 r_free = 0.3962    target_work(ls_wunit_k1) = 0.168         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3962 r_free = 0.3962    target_work(ls_wunit_k1) = 0.168         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3962
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7226
moved from start:          0.3792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12478  Z= 0.156
  Angle     :  0.609   8.294  16915  Z= 0.332
  Chirality :  0.044   0.216   1845
  Planarity :  0.004   0.048   2077
  Dihedral  : 13.968 176.950   1930
  Min Nonbonded Distance : 1.863

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  8.81 %
    Favored  : 91.05 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 14.14 %
    Favored  : 83.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.57 (0.22), residues: 1399
  helix:  0.84 (0.22), residues: 580
  sheet: -1.73 (0.39), residues: 152
  loop : -2.70 (0.22), residues: 667

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 534 
 HIS   0.016   0.001   HIS A 720 
 PHE   0.040   0.002   PHE A1027 
 TYR   0.020   0.002   TYR A1036 
 ARG   0.006   0.000   ARG A 867 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05884 (  496)
  hydrogen bonds       : angle       5.00458 ( 1379)
  SS BOND              : bond        0.01141 (    1)
  SS BOND              : angle       3.47940 (    2)
  covalent geometry    : bond        0.00348 (12477)
  covalent geometry    : angle       0.60815 (16913)

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

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

  2798 Ramachandran restraints generated.
    1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2798 Ramachandran restraints generated.
    1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 188
  time to evaluate  : 1.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 ILE cc_start: 0.7728 (OUTLIER) cc_final: 0.7478 (mt)
REVERT: A  107 LYS cc_start: 0.8138 (tptm) cc_final: 0.7904 (ttpt)
REVERT: A  426 TYR cc_start: 0.6587 (OUTLIER) cc_final: 0.4704 (t80)
REVERT: A  471 LYS cc_start: 0.7853 (tmmt) cc_final: 0.7619 (tttp)
REVERT: A  875 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8296 (tp)
REVERT: A 1133 LEU cc_start: 0.8366 (mp) cc_final: 0.8076 (tp)
REVERT: A 1137 MET cc_start: 0.7167 (ttm) cc_final: 0.6928 (mtp)
REVERT: B  211 VAL cc_start: 0.7749 (OUTLIER) cc_final: 0.7434 (t)
  outliers start: 35
  outliers final: 27
  residues processed: 212
  average time/residue: 0.2699
  time to fit residues: 85.2933
Evaluate side-chains
  209 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 178
  time to evaluate  : 1.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   73 ASN
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  312 SER
Chi-restraints excluded: chain A residue  377 VAL
Chi-restraints excluded: chain A residue  418 ILE
Chi-restraints excluded: chain A residue  426 TYR
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  450 ASP
Chi-restraints excluded: chain A residue  552 LYS
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain A residue  757 VAL
Chi-restraints excluded: chain A residue  802 ILE
Chi-restraints excluded: chain A residue  809 ILE
Chi-restraints excluded: chain A residue  844 VAL
Chi-restraints excluded: chain A residue  875 LEU
Chi-restraints excluded: chain A residue  889 ASN
Chi-restraints excluded: chain A residue 1021 ILE
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  188 TYR
Chi-restraints excluded: chain B residue  192 ASP
Chi-restraints excluded: chain B residue  211 VAL
Chi-restraints excluded: chain B residue  220 ILE
Chi-restraints excluded: chain B residue  229 VAL
Chi-restraints excluded: chain C residue  131 CYS
Chi-restraints excluded: chain C residue  137 ASP
Chi-restraints excluded: chain C residue  225 THR
Chi-restraints excluded: chain C residue  228 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 78 optimal weight:    0.5980
   chunk 54 optimal weight:    3.9990
   chunk 34 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 26 optimal weight:    8.9990
   chunk 96 optimal weight:    1.9990
   chunk 132 optimal weight:    6.9990
   chunk 20 optimal weight:    4.9990
   chunk 7 optimal weight:    6.9990
   chunk 104 optimal weight:    5.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
C 231 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.200136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.166279 restraints weight = 25085.714|
|-----------------------------------------------------------------------------|
r_work (start): 0.3934 rms_B_bonded: 4.01
r_work (final): 0.3934
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3934
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3934 r_free = 0.3934    target_work(ls_wunit_k1) = 0.166         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3934 r_free = 0.3934    target_work(ls_wunit_k1) = 0.166         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3934
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7268
moved from start:          0.3992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  12478  Z= 0.198
  Angle     :  0.659   8.138  16915  Z= 0.357
  Chirality :  0.046   0.226   1845
  Planarity :  0.004   0.056   2077
  Dihedral  : 14.024 175.799   1929
  Min Nonbonded Distance : 1.803

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  9.53 %
    Favored  : 90.33 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 15.15 %
    Favored  : 81.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.48 (0.22), residues: 1399
  helix:  0.92 (0.22), residues: 573
  sheet: -1.71 (0.39), residues: 151
  loop : -2.63 (0.22), residues: 675

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 534 
 HIS   0.019   0.002   HIS A 720 
 PHE   0.037   0.002   PHE A1027 
 TYR   0.021   0.002   TYR A1185 
 ARG   0.005   0.001   ARG A 867 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06568 (  496)
  hydrogen bonds       : angle       5.11860 ( 1379)
  SS BOND              : bond        0.00983 (    1)
  SS BOND              : angle       3.56794 (    2)
  covalent geometry    : bond        0.00452 (12477)
  covalent geometry    : angle       0.65768 (16913)

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

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

  2798 Ramachandran restraints generated.
    1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2798 Ramachandran restraints generated.
    1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 192
  time to evaluate  : 2.191 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 ILE cc_start: 0.7784 (OUTLIER) cc_final: 0.7527 (mt)
REVERT: A  268 GLN cc_start: 0.5498 (mm-40) cc_final: 0.4992 (mt0)
REVERT: A  401 GLN cc_start: 0.7487 (tm-30) cc_final: 0.7065 (tt0)
REVERT: A  426 TYR cc_start: 0.6566 (OUTLIER) cc_final: 0.4560 (t80)
REVERT: A  471 LYS cc_start: 0.7820 (tmmt) cc_final: 0.7547 (tttp)
REVERT: A  875 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8136 (tp)
  outliers start: 43
  outliers final: 34
  residues processed: 222
  average time/residue: 0.4347
  time to fit residues: 147.6518
Evaluate side-chains
  217 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 180
  time to evaluate  : 1.899 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   73 ASN
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  312 SER
Chi-restraints excluded: chain A residue  377 VAL
Chi-restraints excluded: chain A residue  418 ILE
Chi-restraints excluded: chain A residue  426 TYR
Chi-restraints excluded: chain A residue  431 SER
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  450 ASP
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain A residue  485 SER
Chi-restraints excluded: chain A residue  552 LYS
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain A residue  757 VAL
Chi-restraints excluded: chain A residue  802 ILE
Chi-restraints excluded: chain A residue  809 ILE
Chi-restraints excluded: chain A residue  844 VAL
Chi-restraints excluded: chain A residue  868 ILE
Chi-restraints excluded: chain A residue  875 LEU
Chi-restraints excluded: chain A residue  889 ASN
Chi-restraints excluded: chain A residue 1021 ILE
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  192 ASP
Chi-restraints excluded: chain B residue  220 ILE
Chi-restraints excluded: chain B residue  229 VAL
Chi-restraints excluded: chain C residue  131 CYS
Chi-restraints excluded: chain C residue  135 GLU
Chi-restraints excluded: chain C residue  137 ASP
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  225 THR
Chi-restraints excluded: chain C residue  228 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 17 optimal weight:    4.9990
   chunk 136 optimal weight:    1.9990
   chunk 73 optimal weight:    0.6980
   chunk 86 optimal weight:    0.8980
   chunk 134 optimal weight:    9.9990
   chunk 29 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 106 optimal weight:    5.9990
   chunk 70 optimal weight:    3.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
A 231 GLN
A 340 ASN
B 163 GLN
C 125 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.201115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.167707 restraints weight = 32309.961|
|-----------------------------------------------------------------------------|
r_work (start): 0.3941 rms_B_bonded: 4.28
r_work (final): 0.3941
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3942
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3942 r_free = 0.3942    target_work(ls_wunit_k1) = 0.167         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3942 r_free = 0.3942    target_work(ls_wunit_k1) = 0.167         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3942
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7247
moved from start:          0.4146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  12478  Z= 0.182
  Angle     :  0.650   8.514  16915  Z= 0.352
  Chirality :  0.045   0.220   1845
  Planarity :  0.004   0.054   2077
  Dihedral  : 13.990 176.291   1929
  Min Nonbonded Distance : 1.820

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  9.38 %
    Favored  : 90.47 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 15.07 %
    Favored  : 81.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.34 (0.22), residues: 1399
  helix:  1.03 (0.22), residues: 572
  sheet: -1.48 (0.43), residues: 130
  loop : -2.56 (0.21), residues: 697

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 534 
 HIS   0.017   0.002   HIS A 720 
 PHE   0.036   0.002   PHE A1027 
 TYR   0.019   0.002   TYR A1185 
 ARG   0.007   0.001   ARG B 230 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06296 (  496)
  hydrogen bonds       : angle       5.09189 ( 1379)
  SS BOND              : bond        0.00891 (    1)
  SS BOND              : angle       3.25621 (    2)
  covalent geometry    : bond        0.00413 (12477)
  covalent geometry    : angle       0.64933 (16913)

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

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

  2798 Ramachandran restraints generated.
    1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2798 Ramachandran restraints generated.
    1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 183
  time to evaluate  : 1.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 ILE cc_start: 0.7864 (OUTLIER) cc_final: 0.7601 (mt)
REVERT: A  268 GLN cc_start: 0.5536 (mm-40) cc_final: 0.5038 (mt0)
REVERT: A  278 LYS cc_start: 0.7902 (mttp) cc_final: 0.7599 (mtpp)
REVERT: A  401 GLN cc_start: 0.7670 (tm-30) cc_final: 0.7218 (tt0)
REVERT: A  426 TYR cc_start: 0.6351 (OUTLIER) cc_final: 0.4448 (t80)
REVERT: A  471 LYS cc_start: 0.7813 (tmmt) cc_final: 0.7529 (tttp)
REVERT: A  496 ILE cc_start: 0.6322 (OUTLIER) cc_final: 0.6053 (mm)
REVERT: A  765 ILE cc_start: 0.7007 (OUTLIER) cc_final: 0.6210 (tp)
REVERT: A  875 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8133 (tp)
  outliers start: 46
  outliers final: 36
  residues processed: 216
  average time/residue: 0.2284
  time to fit residues: 73.9364
Evaluate side-chains
  213 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 172
  time to evaluate  : 1.789 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   73 ASN
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  109 PHE
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  312 SER
Chi-restraints excluded: chain A residue  377 VAL
Chi-restraints excluded: chain A residue  418 ILE
Chi-restraints excluded: chain A residue  426 TYR
Chi-restraints excluded: chain A residue  431 SER
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  450 ASP
Chi-restraints excluded: chain A residue  485 SER
Chi-restraints excluded: chain A residue  496 ILE
Chi-restraints excluded: chain A residue  552 LYS
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain A residue  757 VAL
Chi-restraints excluded: chain A residue  765 ILE
Chi-restraints excluded: chain A residue  802 ILE
Chi-restraints excluded: chain A residue  809 ILE
Chi-restraints excluded: chain A residue  810 PHE
Chi-restraints excluded: chain A residue  844 VAL
Chi-restraints excluded: chain A residue  875 LEU
Chi-restraints excluded: chain A residue  888 GLN
Chi-restraints excluded: chain A residue  889 ASN
Chi-restraints excluded: chain A residue 1021 ILE
Chi-restraints excluded: chain A residue 1132 SER
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  190 HIS
Chi-restraints excluded: chain B residue  192 ASP
Chi-restraints excluded: chain B residue  220 ILE
Chi-restraints excluded: chain B residue  229 VAL
Chi-restraints excluded: chain C residue  131 CYS
Chi-restraints excluded: chain C residue  135 GLU
Chi-restraints excluded: chain C residue  137 ASP
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  225 THR
Chi-restraints excluded: chain C residue  228 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 57 optimal weight:    4.9990
   chunk 4 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 116 optimal weight:    6.9990
   chunk 134 optimal weight:    7.9990
   chunk 1 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 117 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 25 optimal weight:    6.9990
   chunk 131 optimal weight:    3.9990
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
C 231 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.199584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.166743 restraints weight = 25033.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.3937 rms_B_bonded: 3.90
r_work (final): 0.3937
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3937
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3937 r_free = 0.3937    target_work(ls_wunit_k1) = 0.166         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3937 r_free = 0.3937    target_work(ls_wunit_k1) = 0.166         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3937
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7265
moved from start:          0.4269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  12478  Z= 0.203
  Angle     :  0.678   9.813  16915  Z= 0.366
  Chirality :  0.046   0.223   1845
  Planarity :  0.004   0.054   2077
  Dihedral  : 14.027 175.526   1929
  Min Nonbonded Distance : 1.788

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  9.67 %
    Favored  : 90.26 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 15.07 %
    Favored  : 80.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.36 (0.22), residues: 1399
  helix:  1.00 (0.22), residues: 572
  sheet: -1.46 (0.43), residues: 124
  loop : -2.56 (0.21), residues: 703

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 999 
 HIS   0.019   0.002   HIS A 720 
 PHE   0.051   0.002   PHE A1027 
 TYR   0.020   0.002   TYR A1185 
 ARG   0.007   0.001   ARG B 230 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06708 (  496)
  hydrogen bonds       : angle       5.19891 ( 1379)
  SS BOND              : bond        0.00928 (    1)
  SS BOND              : angle       3.23079 (    2)
  covalent geometry    : bond        0.00468 (12477)
  covalent geometry    : angle       0.67750 (16913)

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

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

  2798 Ramachandran restraints generated.
    1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2798 Ramachandran restraints generated.
    1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 177
  time to evaluate  : 1.267 
Fit side-chains
   revert: symmetry clash
REVERT: A   99 ILE cc_start: 0.7797 (OUTLIER) cc_final: 0.7538 (mt)
REVERT: A  268 GLN cc_start: 0.5505 (mm-40) cc_final: 0.5035 (mt0)
REVERT: A  401 GLN cc_start: 0.7687 (tm-30) cc_final: 0.7225 (tt0)
REVERT: A  426 TYR cc_start: 0.6302 (OUTLIER) cc_final: 0.4519 (t80)
REVERT: A  471 LYS cc_start: 0.7868 (tmmt) cc_final: 0.7573 (tttp)
REVERT: A  496 ILE cc_start: 0.6467 (OUTLIER) cc_final: 0.6126 (mm)
REVERT: A  765 ILE cc_start: 0.7089 (OUTLIER) cc_final: 0.6252 (tp)
REVERT: A  875 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8135 (tp)
  outliers start: 50
  outliers final: 38
  residues processed: 212
  average time/residue: 0.2299
  time to fit residues: 71.9040
Evaluate side-chains
  216 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 173
  time to evaluate  : 1.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   73 ASN
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  109 PHE
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  312 SER
Chi-restraints excluded: chain A residue  418 ILE
Chi-restraints excluded: chain A residue  426 TYR
Chi-restraints excluded: chain A residue  431 SER
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  450 ASP
Chi-restraints excluded: chain A residue  485 SER
Chi-restraints excluded: chain A residue  496 ILE
Chi-restraints excluded: chain A residue  552 LYS
Chi-restraints excluded: chain A residue  680 VAL
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain A residue  757 VAL
Chi-restraints excluded: chain A residue  765 ILE
Chi-restraints excluded: chain A residue  802 ILE
Chi-restraints excluded: chain A residue  809 ILE
Chi-restraints excluded: chain A residue  810 PHE
Chi-restraints excluded: chain A residue  844 VAL
Chi-restraints excluded: chain A residue  868 ILE
Chi-restraints excluded: chain A residue  875 LEU
Chi-restraints excluded: chain A residue  888 GLN
Chi-restraints excluded: chain A residue  889 ASN
Chi-restraints excluded: chain A residue 1021 ILE
Chi-restraints excluded: chain A residue 1132 SER
Chi-restraints excluded: chain A residue 1133 LEU
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  192 ASP
Chi-restraints excluded: chain B residue  220 ILE
Chi-restraints excluded: chain B residue  229 VAL
Chi-restraints excluded: chain C residue  131 CYS
Chi-restraints excluded: chain C residue  137 ASP
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  220 ILE
Chi-restraints excluded: chain C residue  225 THR
Chi-restraints excluded: chain C residue  228 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 27 optimal weight:    0.5980
   chunk 103 optimal weight:    0.8980
   chunk 16 optimal weight:    4.9990
   chunk 43 optimal weight:    0.8980
   chunk 121 optimal weight:    0.9990
   chunk 124 optimal weight:    0.9990
   chunk 113 optimal weight:    0.7980
   chunk 129 optimal weight:    1.9990
   chunk 59 optimal weight:    4.9990
   chunk 26 optimal weight:    6.9990
   chunk 28 optimal weight:    0.5980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 231 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.204027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.169980 restraints weight = 25626.867|
|-----------------------------------------------------------------------------|
r_work (start): 0.3961 rms_B_bonded: 4.02
r_work (final): 0.3961
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3961
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3961 r_free = 0.3961    target_work(ls_wunit_k1) = 0.169         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3961 r_free = 0.3961    target_work(ls_wunit_k1) = 0.169         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3961
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7210
moved from start:          0.4341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  12478  Z= 0.143
  Angle     :  0.626   8.562  16915  Z= 0.338
  Chirality :  0.044   0.211   1845
  Planarity :  0.004   0.053   2077
  Dihedral  : 13.908 177.672   1929
  Min Nonbonded Distance : 1.868

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  8.67 %
    Favored  : 91.19 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 16.39 %
    Favored  : 80.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.09 (0.22), residues: 1399
  helix:  1.24 (0.22), residues: 572
  sheet: -1.20 (0.46), residues: 119
  loop : -2.44 (0.22), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 362 
 HIS   0.011   0.001   HIS A 720 
 PHE   0.059   0.002   PHE A1027 
 TYR   0.016   0.001   TYR C 121 
 ARG   0.009   0.000   ARG B 230 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05542 (  496)
  hydrogen bonds       : angle       4.94863 ( 1379)
  SS BOND              : bond        0.00862 (    1)
  SS BOND              : angle       3.11031 (    2)
  covalent geometry    : bond        0.00316 (12477)
  covalent geometry    : angle       0.62494 (16913)

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

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

  2798 Ramachandran restraints generated.
    1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2798 Ramachandran restraints generated.
    1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 183
  time to evaluate  : 1.435 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 ARG cc_start: 0.7042 (mmt-90) cc_final: 0.6782 (mmt-90)
REVERT: A   99 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.7569 (mt)
REVERT: A  268 GLN cc_start: 0.5337 (mm-40) cc_final: 0.5116 (mt0)
REVERT: A  401 GLN cc_start: 0.7760 (tm-30) cc_final: 0.7277 (tt0)
REVERT: A  426 TYR cc_start: 0.6101 (OUTLIER) cc_final: 0.4307 (t80)
REVERT: A  471 LYS cc_start: 0.7791 (tmmt) cc_final: 0.7512 (tttp)
REVERT: A  482 ARG cc_start: 0.6925 (ptm160) cc_final: 0.6440 (ptm160)
REVERT: A  552 LYS cc_start: 0.5503 (OUTLIER) cc_final: 0.5241 (mtmm)
REVERT: A  875 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8157 (tp)
REVERT: B  137 ASP cc_start: 0.7842 (m-30) cc_final: 0.7627 (m-30)
  outliers start: 35
  outliers final: 27
  residues processed: 208
  average time/residue: 0.2677
  time to fit residues: 85.1787
Evaluate side-chains
  209 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 178
  time to evaluate  : 1.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ASN
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  109 PHE
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  312 SER
Chi-restraints excluded: chain A residue  418 ILE
Chi-restraints excluded: chain A residue  426 TYR
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  450 ASP
Chi-restraints excluded: chain A residue  485 SER
Chi-restraints excluded: chain A residue  552 LYS
Chi-restraints excluded: chain A residue  680 VAL
Chi-restraints excluded: chain A residue  757 VAL
Chi-restraints excluded: chain A residue  802 ILE
Chi-restraints excluded: chain A residue  809 ILE
Chi-restraints excluded: chain A residue  810 PHE
Chi-restraints excluded: chain A residue  875 LEU
Chi-restraints excluded: chain A residue  889 ASN
Chi-restraints excluded: chain A residue 1021 ILE
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  192 ASP
Chi-restraints excluded: chain B residue  220 ILE
Chi-restraints excluded: chain B residue  229 VAL
Chi-restraints excluded: chain C residue  131 CYS
Chi-restraints excluded: chain C residue  137 ASP
Chi-restraints excluded: chain C residue  158 VAL
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  220 ILE
Chi-restraints excluded: chain C residue  225 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 89 optimal weight:    0.0970
   chunk 86 optimal weight:    0.9990
   chunk 126 optimal weight:    2.9990
   chunk 102 optimal weight:    0.9990
   chunk 125 optimal weight:    0.7980
   chunk 121 optimal weight:    3.9990
   chunk 137 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   chunk 21 optimal weight:    6.9990
   chunk 36 optimal weight:    8.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
C 193 GLN
C 231 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.203233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.171328 restraints weight = 32693.732|
|-----------------------------------------------------------------------------|
r_work (start): 0.3978 rms_B_bonded: 4.31
r_work (final): 0.3978
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3981
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3981 r_free = 0.3981    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3981 r_free = 0.3981    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3981
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7178
moved from start:          0.4386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  12478  Z= 0.146
  Angle     :  0.638   8.793  16915  Z= 0.344
  Chirality :  0.044   0.216   1845
  Planarity :  0.004   0.053   2077
  Dihedral  : 13.889 177.084   1929
  Min Nonbonded Distance : 1.855

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  9.46 %
    Favored  : 90.40 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 16.94 %
    Favored  : 80.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.01 (0.22), residues: 1399
  helix:  1.29 (0.22), residues: 571
  sheet: -1.14 (0.45), residues: 125
  loop : -2.38 (0.22), residues: 703

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 362 
 HIS   0.011   0.001   HIS A 720 
 PHE   0.054   0.002   PHE A1027 
 TYR   0.018   0.001   TYR A1036 
 ARG   0.009   0.000   ARG B 230 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05608 (  496)
  hydrogen bonds       : angle       4.96196 ( 1379)
  SS BOND              : bond        0.00809 (    1)
  SS BOND              : angle       3.15446 (    2)
  covalent geometry    : bond        0.00325 (12477)
  covalent geometry    : angle       0.63697 (16913)

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

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

  2798 Ramachandran restraints generated.
    1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2798 Ramachandran restraints generated.
    1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 182
  time to evaluate  : 2.264 
Fit side-chains
   revert: symmetry clash
REVERT: A   99 ILE cc_start: 0.7840 (OUTLIER) cc_final: 0.7571 (mt)
REVERT: A  268 GLN cc_start: 0.5344 (mm-40) cc_final: 0.5045 (mt0)
REVERT: A  401 GLN cc_start: 0.7745 (tm-30) cc_final: 0.7288 (tt0)
REVERT: A  426 TYR cc_start: 0.6190 (OUTLIER) cc_final: 0.4398 (t80)
REVERT: A  471 LYS cc_start: 0.7859 (tmmt) cc_final: 0.7565 (tttp)
REVERT: A  552 LYS cc_start: 0.5488 (OUTLIER) cc_final: 0.5216 (mtmm)
REVERT: A  765 ILE cc_start: 0.6984 (OUTLIER) cc_final: 0.6242 (tp)
REVERT: A  875 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.7963 (mt)
REVERT: B  137 ASP cc_start: 0.7751 (m-30) cc_final: 0.7500 (m-30)
  outliers start: 34
  outliers final: 28
  residues processed: 207
  average time/residue: 0.3396
  time to fit residues: 108.0599
Evaluate side-chains
  206 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 173
  time to evaluate  : 1.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ASN
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  109 PHE
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  312 SER
Chi-restraints excluded: chain A residue  418 ILE
Chi-restraints excluded: chain A residue  426 TYR
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  450 ASP
Chi-restraints excluded: chain A residue  485 SER
Chi-restraints excluded: chain A residue  552 LYS
Chi-restraints excluded: chain A residue  680 VAL
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain A residue  757 VAL
Chi-restraints excluded: chain A residue  765 ILE
Chi-restraints excluded: chain A residue  802 ILE
Chi-restraints excluded: chain A residue  809 ILE
Chi-restraints excluded: chain A residue  810 PHE
Chi-restraints excluded: chain A residue  875 LEU
Chi-restraints excluded: chain A residue  888 GLN
Chi-restraints excluded: chain A residue  889 ASN
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  192 ASP
Chi-restraints excluded: chain B residue  220 ILE
Chi-restraints excluded: chain B residue  229 VAL
Chi-restraints excluded: chain C residue  131 CYS
Chi-restraints excluded: chain C residue  137 ASP
Chi-restraints excluded: chain C residue  158 VAL
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  220 ILE
Chi-restraints excluded: chain C residue  225 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 65 optimal weight:    3.9990
   chunk 92 optimal weight:    0.9990
   chunk 100 optimal weight:    0.7980
   chunk 105 optimal weight:    4.9990
   chunk 118 optimal weight:    5.9990
   chunk 120 optimal weight:    0.7980
   chunk 24 optimal weight:    0.0980
   chunk 107 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 102 optimal weight:    0.6980
   chunk 130 optimal weight:    0.9980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.204315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.170388 restraints weight = 23989.356|
|-----------------------------------------------------------------------------|
r_work (start): 0.3974 rms_B_bonded: 3.95
r_work (final): 0.3974
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3974
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3974 r_free = 0.3974    target_work(ls_wunit_k1) = 0.170         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3974 r_free = 0.3974    target_work(ls_wunit_k1) = 0.170         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3974
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7199
moved from start:          0.4471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  12478  Z= 0.139
  Angle     :  0.627   9.291  16915  Z= 0.337
  Chirality :  0.043   0.174   1845
  Planarity :  0.004   0.053   2077
  Dihedral  : 13.844 177.603   1929
  Min Nonbonded Distance : 1.870

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  8.67 %
    Favored  : 91.19 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 17.33 %
    Favored  : 80.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.94 (0.23), residues: 1399
  helix:  1.36 (0.22), residues: 573
  sheet: -1.26 (0.41), residues: 145
  loop : -2.35 (0.23), residues: 681

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 362 
 HIS   0.010   0.001   HIS A 720 
 PHE   0.051   0.001   PHE A1027 
 TYR   0.015   0.001   TYR C 121 
 ARG   0.009   0.000   ARG B 230 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05335 (  496)
  hydrogen bonds       : angle       4.89477 ( 1379)
  SS BOND              : bond        0.00882 (    1)
  SS BOND              : angle       3.15278 (    2)
  covalent geometry    : bond        0.00308 (12477)
  covalent geometry    : angle       0.62612 (16913)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6764.24 seconds
wall clock time: 123 minutes 2.09 seconds (7382.09 seconds total)