Starting phenix.real_space_refine
on Thu May 15 01:06:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8b9j_15933/05_2025/8b9j_15933.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8b9j_15933/05_2025/8b9j_15933.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.45
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8b9j_15933/05_2025/8b9j_15933.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8b9j_15933/05_2025/8b9j_15933.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8b9j_15933/05_2025/8b9j_15933.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8b9j_15933/05_2025/8b9j_15933.cif"
  }
  resolution = 3.45
  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=   0.001 sd=   0.014
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 6846 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 8
    Type Number    sf(0)   Gaussians
     Al      1      5.89       5
     P       2      5.49       5
     Mg      1      5.21       5
     S      46      5.16       5
     C    4362      2.51       5
     N    1186      2.21       5
     O    1277      1.98       5
     F       4      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 6879
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6846
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 864, 6843
          Classifications: {'peptide': 864}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 821}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
      Conformer: "B"
        Number of residues, atoms: 864, 6843
          Classifications: {'peptide': 864}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 821}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
          bond proxies already assigned to first conformer: 6967
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 33
          Unusual residues: {' MG': 1, 'ADP': 1, 'ALF': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 6.81, per 1000 atoms: 0.99
  Number of scatterers: 6879
  At special positions: 0
  Unit cell: (73.158, 95.352, 101.928, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 8
    Type Number    sf(0)
     S      46     16.00
     P       2     15.00
     Al      1     13.00
     Mg      1     11.99
     F       4      9.00
     O    1277      8.00
     N    1186      7.00
     C    4362      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.69
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1650

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 4 sheets defined
      52.3% alpha, 10.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.78
  Creating SS restraints...
    Processing helix  chain 'A' and resid 268 through 283
    Processing helix  chain 'A' and resid 352 through 371
      removed outlier: 3.510A  pdb=" N   LEU A 356 " --> pdb=" O   SER A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 382
    Processing helix  chain 'A' and resid 384 through 400
      removed outlier: 3.970A  pdb=" N   ALA A 388 " --> pdb=" O   LEU A 384 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   MET A 389 " --> pdb=" O   PRO A 385 " (cutoff:3.500A)
      removed outlier: 4.759A  pdb=" N   SER A 391 " --> pdb=" O   ALA A 387 " (cutoff:3.500A)
      removed outlier: 6.047A  pdb=" N   GLU A 392 " --> pdb=" O   ALA A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 428
    Processing helix  chain 'A' and resid 430 through 433
    Processing helix  chain 'A' and resid 442 through 457
    Processing helix  chain 'A' and resid 487 through 494
    Processing helix  chain 'A' and resid 508 through 512
      removed outlier: 4.042A  pdb=" N   GLU A 511 " --> pdb=" O   GLU A 508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 513 through 530
    Processing helix  chain 'A' and resid 544 through 551
    Processing helix  chain 'A' and resid 570 through 579
    Processing helix  chain 'A' and resid 583 through 600
      removed outlier: 4.835A  pdb=" N   GLU A 596 " --> pdb=" O   GLU A 592 " (cutoff:3.500A)
      removed outlier: 5.795A  pdb=" N   GLU A 597 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   GLN A 598 " --> pdb=" O   GLU A 594 " (cutoff:3.500A)
      removed outlier: 4.269A  pdb=" N   LEU A 600 " --> pdb=" O   GLU A 596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 620 through 630
    Processing helix  chain 'A' and resid 636 through 651
    Processing helix  chain 'A' and resid 662 through 676
    Processing helix  chain 'A' and resid 695 through 704
      removed outlier: 3.807A  pdb=" N   GLN A 699 " --> pdb=" O   PRO A 695 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   LYS A 701 " --> pdb=" O   ASP A 697 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 718 through 721
      removed outlier: 3.877A  pdb=" N   GLU A 721 " --> pdb=" O   ASN A 718 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 718 through 721'
    Processing helix  chain 'A' and resid 758 through 768
    Processing helix  chain 'A' and resid 782 through 789
    Processing helix  chain 'A' and resid 795 through 800
      removed outlier: 3.974A  pdb=" N   THR A 800 " --> pdb=" O   MET A 797 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 802 through 812
    Processing helix  chain 'A' and resid 816 through 823
    Processing helix  chain 'A' and resid 829 through 842
    Processing helix  chain 'A' and resid 865 through 879
    Processing helix  chain 'A' and resid 880 through 892
    Processing helix  chain 'A' and resid 909 through 914
      removed outlier: 3.715A  pdb=" N   LEU A 914 " --> pdb=" O   HIS A 910 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 915 through 919
      removed outlier: 3.637A  pdb=" N   CYS A 919 " --> pdb=" O   GLY A 916 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 920 through 938
    Processing helix  chain 'A' and resid 939 through 950
    Processing helix  chain 'A' and resid 953 through 973
    Processing helix  chain 'A' and resid 977 through 982
      removed outlier: 3.709A  pdb=" N   CYS A 980 " --> pdb=" O   PRO A 977 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   ILE A 982 " --> pdb=" O   GLU A 979 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 994 through 1008
    Processing helix  chain 'A' and resid 1024 through 1026
      No H-bonds generated for 'chain 'A' and resid 1024 through 1026'
    Processing helix  chain 'A' and resid 1070 through 1077
    Processing helix  chain 'A' and resid 1101 through 1125
      Proline residue:  A1113  - end of helix
    Processing helix  chain 'A' and resid 1126 through 1129
      removed outlier: 4.006A  pdb=" N   ILE A1129 " --> pdb=" O   PRO A1126 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1126 through 1129'
    Processing helix  chain 'A' and resid 1133 through 1147
    Processing helix  chain 'A' and resid 1148 through 1153
      removed outlier: 4.416A  pdb=" N   GLY A1152 " --> pdb=" O   LYS A1149 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 263 through 264
      removed outlier: 3.722A  pdb=" N   TYR A 263 " --> pdb=" O   ASN A1097 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   ASP A1099 " --> pdb=" O   TYR A 263 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 472 through 474
      removed outlier: 6.744A  pdb=" N   GLY A 466 " --> pdb=" O   PHE A 484 " (cutoff:3.500A)
      removed outlier: 8.684A  pdb=" N   THR A 486 " --> pdb=" O   GLY A 466 " (cutoff:3.500A)
      removed outlier: 7.654A  pdb=" N   SER A 468 " --> pdb=" O   THR A 486 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   ILE A 436 " --> pdb=" O   LEU A 483 " (cutoff:3.500A)
      removed outlier: 7.229A  pdb=" N   CYS A 485 " --> pdb=" O   ILE A 436 " (cutoff:3.500A)
      removed outlier: 5.541A  pdb=" N   VAL A 438 " --> pdb=" O   CYS A 485 " (cutoff:3.500A)
      removed outlier: 6.011A  pdb=" N   ASN A 435 " --> pdb=" O   HIS A 503 " (cutoff:3.500A)
      removed outlier: 7.541A  pdb=" N   ILE A 505 " --> pdb=" O   ASN A 435 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   TYR A 437 " --> pdb=" O   ILE A 505 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   ILE A 504 " --> pdb=" O   ILE A 536 " (cutoff:3.500A)
      removed outlier: 7.826A  pdb=" N   MET A 538 " --> pdb=" O   ILE A 504 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   VAL A 506 " --> pdb=" O   MET A 538 " (cutoff:3.500A)
      removed outlier: 8.535A  pdb=" N   LEU A 557 " --> pdb=" O   VAL A 402 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   ILE A 404 " --> pdb=" O   LEU A 557 " (cutoff:3.500A)
      removed outlier: 7.605A  pdb=" N   VAL A 559 " --> pdb=" O   ILE A 404 " (cutoff:3.500A)
      removed outlier: 7.031A  pdb=" N   ARG A 406 " --> pdb=" O   VAL A 559 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 566 through 569
      removed outlier: 6.057A  pdb=" N   GLN A 567 " --> pdb=" O   CYS A 777 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   THR A 779 " --> pdb=" O   GLN A 567 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   PHE A 569 " --> pdb=" O   THR A 779 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   LEU A 657 " --> pdb=" O   ILE A 733 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   ILE A 656 " --> pdb=" O   ILE A 714 " (cutoff:3.500A)
      removed outlier: 7.771A  pdb=" N   SER A 716 " --> pdb=" O   ILE A 656 " (cutoff:3.500A)
      removed outlier: 5.849A  pdb=" N   VAL A 658 " --> pdb=" O   SER A 716 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 737 through 740
      removed outlier: 8.295A  pdb=" N   CYS A1063 " --> pdb=" O   ALA A1028 " (cutoff:3.500A)
      removed outlier: 7.053A  pdb=" N   LEU A1030 " --> pdb=" O   CYS A1063 " (cutoff:3.500A)
      removed outlier: 6.971A  pdb=" N   LYS A1020 " --> pdb=" O   LYS A1016 " (cutoff:3.500A)

    321 hydrogen bonds defined for protein.
    927 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.05

  Time building geometry restraints manager: 1.97 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1693
        1.33 -     1.45: 1230
        1.45 -     1.57: 4007
        1.57 -     1.69: 4
        1.69 -     1.82: 74
  Bond restraints: 7008
  Sorted by residual:
  bond pdb=" F3  ALF A1202 "
       pdb="AL   ALF A1202 "
    ideal  model  delta    sigma   weight residual
    1.685  1.784 -0.099 2.00e-02 2.50e+03 2.46e+01
  bond pdb=" F1  ALF A1202 "
       pdb="AL   ALF A1202 "
    ideal  model  delta    sigma   weight residual
    1.684  1.783 -0.099 2.00e-02 2.50e+03 2.45e+01
  bond pdb=" F2  ALF A1202 "
       pdb="AL   ALF A1202 "
    ideal  model  delta    sigma   weight residual
    1.685  1.783 -0.098 2.00e-02 2.50e+03 2.41e+01
  bond pdb=" F4  ALF A1202 "
       pdb="AL   ALF A1202 "
    ideal  model  delta    sigma   weight residual
    1.686  1.783 -0.097 2.00e-02 2.50e+03 2.36e+01
  bond pdb=" N   VAL A 772 "
       pdb=" CA  VAL A 772 "
    ideal  model  delta    sigma   weight residual
    1.459  1.500 -0.041 1.25e-02 6.40e+03 1.08e+01
  ... (remaining 7003 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    14.24: 9492
       14.24 -    28.49: 4
       28.49 -    42.73: 0
       42.73 -    56.97: 0
       56.97 -    71.21: 2
  Bond angle restraints: 9498
  Sorted by residual:
  angle pdb=" F1  ALF A1202 "
        pdb="AL   ALF A1202 "
        pdb=" F2  ALF A1202 "
      ideal   model   delta    sigma   weight residual
     108.68  179.89  -71.21 3.00e+00 1.11e-01 5.63e+02
  angle pdb=" F3  ALF A1202 "
        pdb="AL   ALF A1202 "
        pdb=" F4  ALF A1202 "
      ideal   model   delta    sigma   weight residual
     109.63  179.36  -69.73 3.00e+00 1.11e-01 5.40e+02
  angle pdb=" CA  PRO A 653 "
        pdb=" N   PRO A 653 "
        pdb=" CD  PRO A 653 "
      ideal   model   delta    sigma   weight residual
     112.00   99.57   12.43 1.40e+00 5.10e-01 7.88e+01
  angle pdb=" C   GLN A 567 "
        pdb=" N   GLN A 568 "
        pdb=" CA  GLN A 568 "
      ideal   model   delta    sigma   weight residual
     123.05  110.76   12.29 1.40e+00 5.10e-01 7.70e+01
  angle pdb=" F2  ALF A1202 "
        pdb="AL   ALF A1202 "
        pdb=" F4  ALF A1202 "
      ideal   model   delta    sigma   weight residual
     110.21   90.00   20.21 3.00e+00 1.11e-01 4.54e+01
  ... (remaining 9493 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.69: 3638
       17.69 -    35.38: 493
       35.38 -    53.07: 134
       53.07 -    70.76: 26
       70.76 -    88.45: 6
  Dihedral angle restraints: 4297
    sinusoidal: 1766
      harmonic: 2531
  Sorted by residual:
  dihedral pdb=" CD  ARG A 773 "
           pdb=" NE  ARG A 773 "
           pdb=" CZ  ARG A 773 "
           pdb=" NH1 ARG A 773 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   60.89  -60.89     1      1.00e+01 1.00e-02 4.93e+01
  dihedral pdb=" CA  GLU A 842 "
           pdb=" C   GLU A 842 "
           pdb=" N   MET A 843 "
           pdb=" CA  MET A 843 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.16  -25.84     0      5.00e+00 4.00e-02 2.67e+01
  dihedral pdb=" CD  ARG A 562 "
           pdb=" NE  ARG A 562 "
           pdb=" CZ  ARG A 562 "
           pdb=" NH1 ARG A 562 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   33.69  -33.69     1      1.00e+01 1.00e-02 1.61e+01
  ... (remaining 4294 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 891
       0.056 -    0.112: 169
       0.112 -    0.168: 25
       0.168 -    0.223: 3
       0.223 -    0.279: 4
  Chirality restraints: 1092
  Sorted by residual:
  chirality pdb=" CA  ARG A 773 "
            pdb=" N   ARG A 773 "
            pdb=" C   ARG A 773 "
            pdb=" CB  ARG A 773 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.28 2.00e-01 2.50e+01 1.95e+00
  chirality pdb=" CA  GLN A 567 "
            pdb=" N   GLN A 567 "
            pdb=" C   GLN A 567 "
            pdb=" CB  GLN A 567 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.78   -0.27 2.00e-01 2.50e+01 1.77e+00
  chirality pdb=" CA  PHE A 564 "
            pdb=" N   PHE A 564 "
            pdb=" C   PHE A 564 "
            pdb=" CB  PHE A 564 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.44e+00
  ... (remaining 1089 not shown)

  Planarity restraints: 1219
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 773 "   -0.962 9.50e-02 1.11e+02   4.31e-01 1.13e+02
        pdb=" NE  ARG A 773 "    0.057 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 773 "    0.013 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 773 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 773 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 562 "    0.598 9.50e-02 1.11e+02   2.68e-01 4.39e+01
        pdb=" NE  ARG A 562 "   -0.036 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 562 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 562 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 562 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 652 "    0.071 5.00e-02 4.00e+02   9.97e-02 1.59e+01
        pdb=" N   PRO A 653 "   -0.172 5.00e-02 4.00e+02
        pdb=" CA  PRO A 653 "    0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO A 653 "    0.056 5.00e-02 4.00e+02
  ... (remaining 1216 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.60: 65
        2.60 -     3.17: 5955
        3.17 -     3.75: 10797
        3.75 -     4.32: 14237
        4.32 -     4.90: 23895
  Nonbonded interactions: 54949
  Sorted by model distance:
  nonbonded pdb=" O   ILE A 724 "
            pdb="MG    MG A1203 "
     model   vdw
     2.019 2.170
  nonbonded pdb=" OG1 THR A 676 "
            pdb=" O   PHE A 679 "
     model   vdw
     2.153 3.040
  nonbonded pdb=" O3B ADP A1201 "
            pdb=" F3  ALF A1202 "
     model   vdw
     2.193 2.990
  nonbonded pdb=" NZ  LYS A 413 "
            pdb=" F4  ALF A1202 "
     model   vdw
     2.196 3.070
  nonbonded pdb=" OG  SER A 448 "
            pdb=" N6  ADP A1201 "
     model   vdw
     2.225 3.120
  ... (remaining 54944 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             0.850
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     21.760
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.570
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7275
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   0.151   7009  Z= 0.295
  Angle     :  1.365  71.213   9498  Z= 0.578
  Chirality :  0.048   0.279   1092
  Planarity :  0.016   0.431   1219
  Dihedral  : 17.470  88.445   2647
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 13.74
  Ramachandran Plot:
    Outliers :  0.70 %
    Allowed  :  7.24 %
    Favored  : 92.06 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 24.74 %
    Favored  : 74.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    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: -0.47 (0.29), residues: 857
  helix:  0.70 (0.26), residues: 400
  sheet: -1.05 (0.50), residues: 106
  loop : -1.18 (0.36), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 949 
 HIS   0.003   0.001   HIS A 941 
 PHE   0.031   0.002   PHE A 672 
 TYR   0.009   0.001   TYR A 550 
 ARG   0.013   0.001   ARG A 938 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14376 (  321)
  hydrogen bonds       : angle       5.67369 (  927)
  covalent geometry    : bond        0.00481 ( 7008)
  covalent geometry    : angle       1.36541 ( 9498)
  Misc. bond           : bond        0.15123 (    1)

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 67
  time to evaluate  : 0.857 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  679 PHE cc_start: 0.6036 (m-80) cc_final: 0.5590 (m-10)
  outliers start: 8
  outliers final: 4
  residues processed: 74
  average time/residue: 0.2068
  time to fit residues: 20.8182
Evaluate side-chains
  48 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 44
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  567 GLN
Chi-restraints excluded: chain A residue  740 MET
Chi-restraints excluded: chain A residue  772 VAL
Chi-restraints excluded: chain A residue  902 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    0.0040
   chunk 65 optimal weight:   10.0000
   chunk 36 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 67 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 40 optimal weight:    0.8980
   chunk 50 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9980
   overall best weight:    0.7392

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

Flipped N/Q/H residues before XYZ refinement:
** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 674 GLN
** A 910 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 958 ASN
A1037 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.079081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.057508 restraints weight = 33676.177|
|-----------------------------------------------------------------------------|
r_work (start): 0.3122 rms_B_bonded: 5.92
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3122
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3122 r_free = 0.3122    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3122 r_free = 0.3122    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3122
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.1383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070   7009  Z= 0.138
  Angle     :  0.711   7.967   9498  Z= 0.353
  Chirality :  0.044   0.147   1092
  Planarity :  0.005   0.057   1219
  Dihedral  :  5.956  52.309    955
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  8.06 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 24.35 %
    Favored  : 73.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    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:  0.07 (0.30), residues: 857
  helix:  1.32 (0.26), residues: 396
  sheet: -0.87 (0.54), residues: 100
  loop : -1.10 (0.35), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 949 
 HIS   0.005   0.001   HIS A 984 
 PHE   0.017   0.001   PHE A 518 
 TYR   0.014   0.001   TYR A1009 
 ARG   0.008   0.001   ARG A 590 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03931 (  321)
  hydrogen bonds       : angle       4.46757 (  927)
  covalent geometry    : bond        0.00317 ( 7008)
  covalent geometry    : angle       0.71102 ( 9498)
  Misc. bond           : bond        0.00152 (    1)

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 46
  time to evaluate  : 0.833 
Fit side-chains
   revert: symmetry clash
REVERT: A  378 LEU cc_start: 0.9558 (OUTLIER) cc_final: 0.9357 (mm)
  outliers start: 14
  outliers final: 4
  residues processed: 59
  average time/residue: 0.1400
  time to fit residues: 12.7350
Evaluate side-chains
  47 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 42
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  665 LEU
Chi-restraints excluded: chain A residue  690 CYS
Chi-restraints excluded: chain A residue  762 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 44 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9980
   chunk 13 optimal weight:    3.9990
   chunk 64 optimal weight:   10.0000
   chunk 1 optimal weight:    5.9990
   chunk 21 optimal weight:    0.5980
   chunk 7 optimal weight:    7.9990
   chunk 38 optimal weight:   20.0000
   chunk 23 optimal weight:    0.9980
   chunk 75 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   overall best weight:    1.2982

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

Flipped N/Q/H residues before XYZ refinement:
** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 910 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.078462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.056702 restraints weight = 45388.312|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 6.63
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3162
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3162 r_free = 0.3162    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3162 r_free = 0.3162    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3162
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8188
moved from start:          0.1775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7009  Z= 0.138
  Angle     :  0.668  10.614   9498  Z= 0.329
  Chirality :  0.044   0.161   1092
  Planarity :  0.005   0.045   1219
  Dihedral  :  4.992  41.136    946
  Min Nonbonded Distance : 1.940

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  7.01 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 22.77 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    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:  0.33 (0.30), residues: 857
  helix:  1.47 (0.26), residues: 403
  sheet: -0.75 (0.52), residues: 106
  loop : -0.91 (0.36), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 663 
 HIS   0.004   0.001   HIS A 984 
 PHE   0.013   0.001   PHE A 518 
 TYR   0.026   0.001   TYR A1009 
 ARG   0.005   0.000   ARG A 587 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03655 (  321)
  hydrogen bonds       : angle       4.27601 (  927)
  covalent geometry    : bond        0.00324 ( 7008)
  covalent geometry    : angle       0.66819 ( 9498)
  Misc. bond           : bond        0.00015 (    1)

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 42
  time to evaluate  : 0.809 
Fit side-chains
   revert: symmetry clash
REVERT: A  378 LEU cc_start: 0.9586 (OUTLIER) cc_final: 0.9361 (mm)
REVERT: A  645 MET cc_start: 0.9164 (mmm) cc_final: 0.8688 (mmm)
  outliers start: 15
  outliers final: 7
  residues processed: 53
  average time/residue: 0.1411
  time to fit residues: 11.8208
Evaluate side-chains
  47 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 39
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  465 VAL
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain A residue  665 LEU
Chi-restraints excluded: chain A residue  690 CYS
Chi-restraints excluded: chain A residue  740 MET
Chi-restraints excluded: chain A residue  762 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 83 optimal weight:    0.0020
   chunk 39 optimal weight:    0.6980
   chunk 26 optimal weight:    4.9990
   chunk 3 optimal weight:    0.5980
   chunk 32 optimal weight:    0.6980
   chunk 30 optimal weight:    7.9990
   chunk 21 optimal weight:    0.9980
   chunk 40 optimal weight:    0.8980
   chunk 51 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 63 optimal weight:    3.9990
   overall best weight:    0.5788

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

Flipped N/Q/H residues before XYZ refinement:
** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 910 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.079384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.057962 restraints weight = 28536.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.3118 rms_B_bonded: 5.57
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3120
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3120 r_free = 0.3120    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3120 r_free = 0.3120    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3120
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.2106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7009  Z= 0.114
  Angle     :  0.633  10.976   9498  Z= 0.312
  Chirality :  0.043   0.280   1092
  Planarity :  0.004   0.045   1219
  Dihedral  :  4.895  41.465    946
  Min Nonbonded Distance : 2.032

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  7.13 %
    Favored  : 92.52 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 22.51 %
    Favored  : 75.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    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:  0.50 (0.30), residues: 857
  helix:  1.61 (0.26), residues: 404
  sheet: -0.41 (0.54), residues: 98
  loop : -0.94 (0.36), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 949 
 HIS   0.004   0.001   HIS A 984 
 PHE   0.010   0.001   PHE A 518 
 TYR   0.007   0.001   TYR A 619 
 ARG   0.003   0.000   ARG A 768 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03303 (  321)
  hydrogen bonds       : angle       4.04508 (  927)
  covalent geometry    : bond        0.00259 ( 7008)
  covalent geometry    : angle       0.63304 ( 9498)
  Misc. bond           : bond        0.00014 (    1)

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 42
  time to evaluate  : 0.795 
Fit side-chains
   revert: symmetry clash
REVERT: A  645 MET cc_start: 0.9264 (mmm) cc_final: 0.8811 (mmm)
REVERT: A  844 ARG cc_start: 0.4648 (OUTLIER) cc_final: 0.4419 (mtm-85)
REVERT: A  965 GLN cc_start: 0.7557 (OUTLIER) cc_final: 0.7073 (mp10)
REVERT: A  973 GLN cc_start: 0.9401 (OUTLIER) cc_final: 0.9180 (mp10)
REVERT: A  981 MET cc_start: 0.8282 (mtp) cc_final: 0.8023 (mpp)
  outliers start: 15
  outliers final: 6
  residues processed: 55
  average time/residue: 0.1839
  time to fit residues: 14.4939
Evaluate side-chains
  48 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 39
  time to evaluate  : 0.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  465 VAL
Chi-restraints excluded: chain A residue  635 VAL
Chi-restraints excluded: chain A residue  665 LEU
Chi-restraints excluded: chain A residue  690 CYS
Chi-restraints excluded: chain A residue  740 MET
Chi-restraints excluded: chain A residue  844 ARG
Chi-restraints excluded: chain A residue  965 GLN
Chi-restraints excluded: chain A residue  973 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 59 optimal weight:    5.9990
   chunk 83 optimal weight:   10.0000
   chunk 5 optimal weight:    0.4980
   chunk 10 optimal weight:    6.9990
   chunk 46 optimal weight:    5.9990
   chunk 64 optimal weight:    9.9990
   chunk 11 optimal weight:    4.9990
   chunk 81 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 910 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 958 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.077123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.054707 restraints weight = 41950.789|
|-----------------------------------------------------------------------------|
r_work (start): 0.3038 rms_B_bonded: 6.64
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3037
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3037 r_free = 0.3037    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3037 r_free = 0.3037    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3037
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.2264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7009  Z= 0.152
  Angle     :  0.659  10.267   9498  Z= 0.320
  Chirality :  0.044   0.234   1092
  Planarity :  0.004   0.044   1219
  Dihedral  :  4.921  40.605    946
  Min Nonbonded Distance : 1.911

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  7.01 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 22.25 %
    Favored  : 75.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    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:  0.49 (0.30), residues: 857
  helix:  1.71 (0.26), residues: 404
  sheet: -0.44 (0.55), residues: 98
  loop : -1.08 (0.36), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 932 
 HIS   0.004   0.001   HIS A 984 
 PHE   0.012   0.001   PHE A 518 
 TYR   0.009   0.001   TYR A 467 
 ARG   0.003   0.000   ARG A 773 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03554 (  321)
  hydrogen bonds       : angle       4.11438 (  927)
  covalent geometry    : bond        0.00362 ( 7008)
  covalent geometry    : angle       0.65912 ( 9498)
  Misc. bond           : bond        0.00023 (    1)

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 37
  time to evaluate  : 0.747 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  645 MET cc_start: 0.9301 (mmm) cc_final: 0.8848 (mmm)
REVERT: A  844 ARG cc_start: 0.5004 (OUTLIER) cc_final: 0.4676 (mtm-85)
REVERT: A  965 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.7158 (mp10)
REVERT: A  981 MET cc_start: 0.8319 (mtp) cc_final: 0.8015 (mpp)
  outliers start: 15
  outliers final: 10
  residues processed: 50
  average time/residue: 0.1570
  time to fit residues: 11.7642
Evaluate side-chains
  48 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 36
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  389 MET
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  465 VAL
Chi-restraints excluded: chain A residue  635 VAL
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain A residue  665 LEU
Chi-restraints excluded: chain A residue  690 CYS
Chi-restraints excluded: chain A residue  762 LEU
Chi-restraints excluded: chain A residue  844 ARG
Chi-restraints excluded: chain A residue  965 GLN
Chi-restraints excluded: chain A residue  973 GLN
Chi-restraints excluded: chain A residue 1006 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 2 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 48 optimal weight:    7.9990
   chunk 55 optimal weight:    0.9980
   chunk 64 optimal weight:    5.9990
   chunk 9 optimal weight:    9.9990
   chunk 76 optimal weight:    0.0570
   chunk 7 optimal weight:    9.9990
   chunk 66 optimal weight:    4.9990
   chunk 74 optimal weight:    0.0010
   chunk 15 optimal weight:    0.6980
   overall best weight:    0.7506

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

Flipped N/Q/H residues before XYZ refinement:
** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 910 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.078306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.057773 restraints weight = 23415.975|
|-----------------------------------------------------------------------------|
r_work (start): 0.3126 rms_B_bonded: 5.05
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3127
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3127 r_free = 0.3127    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3127 r_free = 0.3127    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3127
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.2451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7009  Z= 0.112
  Angle     :  0.633  10.250   9498  Z= 0.306
  Chirality :  0.043   0.222   1092
  Planarity :  0.004   0.044   1219
  Dihedral  :  4.821  39.306    946
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  7.13 %
    Favored  : 92.52 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 22.77 %
    Favored  : 75.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    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:  0.62 (0.30), residues: 857
  helix:  1.80 (0.26), residues: 404
  sheet: -0.31 (0.56), residues: 98
  loop : -1.03 (0.36), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 663 
 HIS   0.005   0.001   HIS A 984 
 PHE   0.010   0.001   PHE A 518 
 TYR   0.013   0.001   TYR A1009 
 ARG   0.003   0.000   ARG A 773 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03195 (  321)
  hydrogen bonds       : angle       3.93017 (  927)
  covalent geometry    : bond        0.00264 ( 7008)
  covalent geometry    : angle       0.63277 ( 9498)
  Misc. bond           : bond        0.00017 (    1)

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 37
  time to evaluate  : 0.732 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  645 MET cc_start: 0.9285 (mmm) cc_final: 0.8815 (mmm)
REVERT: A  844 ARG cc_start: 0.4837 (OUTLIER) cc_final: 0.4589 (mtm-85)
REVERT: A  965 GLN cc_start: 0.7666 (OUTLIER) cc_final: 0.7237 (mp10)
REVERT: A  981 MET cc_start: 0.8258 (mtp) cc_final: 0.8020 (mpp)
  outliers start: 14
  outliers final: 8
  residues processed: 49
  average time/residue: 0.1553
  time to fit residues: 11.4565
Evaluate side-chains
  43 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 33
  time to evaluate  : 0.729 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  389 MET
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  465 VAL
Chi-restraints excluded: chain A residue  635 VAL
Chi-restraints excluded: chain A residue  665 LEU
Chi-restraints excluded: chain A residue  690 CYS
Chi-restraints excluded: chain A residue  844 ARG
Chi-restraints excluded: chain A residue  965 GLN
Chi-restraints excluded: chain A residue  973 GLN
Chi-restraints excluded: chain A residue 1006 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 33 optimal weight:    9.9990
   chunk 19 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 73 optimal weight:    9.9990
   chunk 80 optimal weight:    0.0370
   chunk 28 optimal weight:    3.9990
   chunk 20 optimal weight:    0.7980
   chunk 61 optimal weight:    4.9990
   chunk 79 optimal weight:    4.9990
   chunk 81 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   overall best weight:    0.9262

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

Flipped N/Q/H residues before XYZ refinement:
** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 910 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.077981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.055664 restraints weight = 41823.525|
|-----------------------------------------------------------------------------|
r_work (start): 0.3065 rms_B_bonded: 6.67
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3066
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3066 r_free = 0.3066    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3066 r_free = 0.3066    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3066
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.2624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7009  Z= 0.116
  Angle     :  0.638  10.039   9498  Z= 0.305
  Chirality :  0.043   0.213   1092
  Planarity :  0.004   0.042   1219
  Dihedral  :  4.798  39.738    946
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  6.66 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 22.51 %
    Favored  : 75.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    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:  0.66 (0.30), residues: 857
  helix:  1.79 (0.26), residues: 404
  sheet: -0.20 (0.56), residues: 98
  loop : -0.98 (0.36), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 932 
 HIS   0.005   0.001   HIS A 984 
 PHE   0.011   0.001   PHE A 518 
 TYR   0.013   0.001   TYR A1009 
 ARG   0.003   0.000   ARG A 768 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03224 (  321)
  hydrogen bonds       : angle       3.93108 (  927)
  covalent geometry    : bond        0.00273 ( 7008)
  covalent geometry    : angle       0.63850 ( 9498)
  Misc. bond           : bond        0.00017 (    1)

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 34
  time to evaluate  : 0.733 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  645 MET cc_start: 0.9302 (mmm) cc_final: 0.8857 (mmm)
REVERT: A  734 ASP cc_start: 0.7340 (t0) cc_final: 0.6932 (t70)
REVERT: A  844 ARG cc_start: 0.4865 (OUTLIER) cc_final: 0.4606 (mtm-85)
REVERT: A  965 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.7261 (mp10)
  outliers start: 13
  outliers final: 9
  residues processed: 45
  average time/residue: 0.1717
  time to fit residues: 11.4717
Evaluate side-chains
  45 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 34
  time to evaluate  : 0.745 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  389 MET
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  465 VAL
Chi-restraints excluded: chain A residue  635 VAL
Chi-restraints excluded: chain A residue  665 LEU
Chi-restraints excluded: chain A residue  690 CYS
Chi-restraints excluded: chain A residue  762 LEU
Chi-restraints excluded: chain A residue  844 ARG
Chi-restraints excluded: chain A residue  965 GLN
Chi-restraints excluded: chain A residue  973 GLN
Chi-restraints excluded: chain A residue 1006 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 10 optimal weight:    6.9990
   chunk 12 optimal weight:    2.9990
   chunk 31 optimal weight:    9.9990
   chunk 61 optimal weight:    4.9990
   chunk 77 optimal weight:    5.9990
   chunk 25 optimal weight:    0.5980
   chunk 42 optimal weight:    3.9990
   chunk 53 optimal weight:    0.5980
   chunk 67 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   overall best weight:    2.2386

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

Flipped N/Q/H residues before XYZ refinement:
** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 910 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 941 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.075657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.053216 restraints weight = 46062.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.2997 rms_B_bonded: 6.84
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2995
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2995 r_free = 0.2995    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2995 r_free = 0.2995    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2995
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.2667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7009  Z= 0.180
  Angle     :  0.687   9.810   9498  Z= 0.329
  Chirality :  0.044   0.194   1092
  Planarity :  0.004   0.042   1219
  Dihedral  :  4.953  39.875    946
  Min Nonbonded Distance : 1.937

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  7.13 %
    Favored  : 92.52 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 22.12 %
    Favored  : 75.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    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:  0.56 (0.30), residues: 857
  helix:  1.68 (0.26), residues: 404
  sheet: -0.37 (0.55), residues: 98
  loop : -0.95 (0.36), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 932 
 HIS   0.005   0.001   HIS A 984 
 PHE   0.017   0.001   PHE A 518 
 TYR   0.012   0.001   TYR A 619 
 ARG   0.003   0.000   ARG A 773 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03689 (  321)
  hydrogen bonds       : angle       4.13442 (  927)
  covalent geometry    : bond        0.00424 ( 7008)
  covalent geometry    : angle       0.68665 ( 9498)
  Misc. bond           : bond        0.00055 (    1)

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 32
  time to evaluate  : 0.815 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  645 MET cc_start: 0.9300 (mmm) cc_final: 0.8871 (mmm)
REVERT: A  734 ASP cc_start: 0.7588 (t0) cc_final: 0.7211 (t70)
REVERT: A  844 ARG cc_start: 0.5288 (OUTLIER) cc_final: 0.4939 (mtm-85)
REVERT: A  965 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.7262 (mt0)
  outliers start: 15
  outliers final: 10
  residues processed: 45
  average time/residue: 0.1625
  time to fit residues: 10.9813
Evaluate side-chains
  44 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 32
  time to evaluate  : 0.738 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  465 VAL
Chi-restraints excluded: chain A residue  635 VAL
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain A residue  660 LEU
Chi-restraints excluded: chain A residue  665 LEU
Chi-restraints excluded: chain A residue  690 CYS
Chi-restraints excluded: chain A residue  762 LEU
Chi-restraints excluded: chain A residue  844 ARG
Chi-restraints excluded: chain A residue  965 GLN
Chi-restraints excluded: chain A residue  973 GLN
Chi-restraints excluded: chain A residue 1006 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 67 optimal weight:    0.8980
   chunk 72 optimal weight:    4.9990
   chunk 5 optimal weight:    0.0670
   chunk 7 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 24 optimal weight:    0.3980
   chunk 39 optimal weight:    0.5980
   chunk 17 optimal weight:    0.0770
   overall best weight:    0.3876

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

Flipped N/Q/H residues before XYZ refinement:
** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 941 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.078333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.058124 restraints weight = 23197.262|
|-----------------------------------------------------------------------------|
r_work (start): 0.3128 rms_B_bonded: 5.00
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3131
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3131 r_free = 0.3131    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3131 r_free = 0.3131    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3131
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.2823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   7009  Z= 0.106
  Angle     :  0.641   9.931   9498  Z= 0.307
  Chirality :  0.043   0.201   1092
  Planarity :  0.004   0.043   1219
  Dihedral  :  4.858  39.967    946
  Min Nonbonded Distance : 2.041

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  7.24 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 22.77 %
    Favored  : 75.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    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:  0.71 (0.31), residues: 857
  helix:  1.78 (0.26), residues: 398
  sheet: -0.10 (0.57), residues: 96
  loop : -0.84 (0.36), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 932 
 HIS   0.005   0.001   HIS A 984 
 PHE   0.014   0.001   PHE A 518 
 TYR   0.015   0.001   TYR A1009 
 ARG   0.003   0.000   ARG A 768 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03094 (  321)
  hydrogen bonds       : angle       3.94603 (  927)
  covalent geometry    : bond        0.00243 ( 7008)
  covalent geometry    : angle       0.64094 ( 9498)
  Misc. bond           : bond        0.00018 (    1)

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 34
  time to evaluate  : 0.942 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  645 MET cc_start: 0.9286 (mmm) cc_final: 0.8831 (mmm)
REVERT: A  844 ARG cc_start: 0.4801 (OUTLIER) cc_final: 0.4562 (mtm-85)
REVERT: A  931 MET cc_start: 0.9027 (ptm) cc_final: 0.8492 (ppp)
REVERT: A  965 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.7321 (mp10)
  outliers start: 10
  outliers final: 7
  residues processed: 43
  average time/residue: 0.1658
  time to fit residues: 10.7108
Evaluate side-chains
  43 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 34
  time to evaluate  : 0.714 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  465 VAL
Chi-restraints excluded: chain A residue  635 VAL
Chi-restraints excluded: chain A residue  660 LEU
Chi-restraints excluded: chain A residue  665 LEU
Chi-restraints excluded: chain A residue  844 ARG
Chi-restraints excluded: chain A residue  965 GLN
Chi-restraints excluded: chain A residue  973 GLN
Chi-restraints excluded: chain A residue 1006 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 31 optimal weight:    7.9990
   chunk 5 optimal weight:    5.9990
   chunk 75 optimal weight:    0.0870
   chunk 34 optimal weight:    0.0670
   chunk 22 optimal weight:    0.0970
   chunk 51 optimal weight:    0.4980
   chunk 85 optimal weight:    1.9990
   chunk 40 optimal weight:    4.9990
   overall best weight:    0.3294

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

Flipped N/Q/H residues before XYZ refinement:
** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.078960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.057661 restraints weight = 29800.199|
|-----------------------------------------------------------------------------|
r_work (start): 0.3122 rms_B_bonded: 5.71
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3122
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3122 r_free = 0.3122    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3122 r_free = 0.3122    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3122
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.2969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   7009  Z= 0.103
  Angle     :  0.630   9.955   9498  Z= 0.302
  Chirality :  0.043   0.200   1092
  Planarity :  0.004   0.043   1219
  Dihedral  :  4.742  40.384    946
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  6.31 %
    Favored  : 93.34 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 22.64 %
    Favored  : 75.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    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:  0.80 (0.31), residues: 857
  helix:  1.82 (0.26), residues: 398
  sheet: -0.06 (0.54), residues: 108
  loop : -0.78 (0.37), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 932 
 HIS   0.005   0.001   HIS A 984 
 PHE   0.011   0.001   PHE A 946 
 TYR   0.014   0.001   TYR A1009 
 ARG   0.003   0.000   ARG A 768 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03033 (  321)
  hydrogen bonds       : angle       3.89414 (  927)
  covalent geometry    : bond        0.00235 ( 7008)
  covalent geometry    : angle       0.63014 ( 9498)
  Misc. bond           : bond        0.00014 (    1)

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 35
  time to evaluate  : 0.820 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  645 MET cc_start: 0.9290 (mmm) cc_final: 0.8836 (mmm)
REVERT: A  844 ARG cc_start: 0.4778 (OUTLIER) cc_final: 0.4559 (mtm-85)
REVERT: A  931 MET cc_start: 0.9018 (ptm) cc_final: 0.8508 (ppp)
  outliers start: 10
  outliers final: 7
  residues processed: 43
  average time/residue: 0.1739
  time to fit residues: 11.2324
Evaluate side-chains
  42 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 34
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  465 VAL
Chi-restraints excluded: chain A residue  635 VAL
Chi-restraints excluded: chain A residue  660 LEU
Chi-restraints excluded: chain A residue  665 LEU
Chi-restraints excluded: chain A residue  844 ARG
Chi-restraints excluded: chain A residue  973 GLN
Chi-restraints excluded: chain A residue 1006 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 82 optimal weight:    0.9990
   chunk 81 optimal weight:    0.3980
   chunk 67 optimal weight:    0.8980
   chunk 78 optimal weight:    3.9990
   chunk 44 optimal weight:    0.6980
   chunk 26 optimal weight:    0.8980
   chunk 71 optimal weight:    0.0470
   chunk 65 optimal weight:    8.9990
   chunk 80 optimal weight:    0.0970
   chunk 42 optimal weight:    4.9990
   chunk 3 optimal weight:    7.9990
   overall best weight:    0.4276

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

Flipped N/Q/H residues before XYZ refinement:
** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.078982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.056541 restraints weight = 46081.742|
|-----------------------------------------------------------------------------|
r_work (start): 0.3118 rms_B_bonded: 7.03
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3120
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3120 r_free = 0.3120    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3120 r_free = 0.3120    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3120
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.3063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   7009  Z= 0.103
  Angle     :  0.633   9.918   9498  Z= 0.302
  Chirality :  0.043   0.198   1092
  Planarity :  0.004   0.043   1219
  Dihedral  :  4.693  41.034    946
  Min Nonbonded Distance : 2.050

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  6.78 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 22.51 %
    Favored  : 76.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    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:  0.83 (0.31), residues: 857
  helix:  1.82 (0.26), residues: 399
  sheet: -0.03 (0.54), residues: 108
  loop : -0.73 (0.37), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 932 
 HIS   0.006   0.001   HIS A 984 
 PHE   0.012   0.001   PHE A 518 
 TYR   0.014   0.001   TYR A1009 
 ARG   0.003   0.000   ARG A 768 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02991 (  321)
  hydrogen bonds       : angle       3.91125 (  927)
  covalent geometry    : bond        0.00236 ( 7008)
  covalent geometry    : angle       0.63254 ( 9498)
  Misc. bond           : bond        0.00019 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3384.77 seconds
wall clock time: 59 minutes 52.19 seconds (3592.19 seconds total)