Starting phenix.real_space_refine
on Wed Jul 30 15:18:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8b9j_15933/07_2025/8b9j_15933.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8b9j_15933/07_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_15933/07_2025/8b9j_15933.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8b9j_15933/07_2025/8b9j_15933.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8b9j_15933/07_2025/8b9j_15933.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8b9j_15933/07_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-5711/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: 7.58, per 1000 atoms: 1.10
  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: 1.97
  Conformation dependent library (CDL) restraints added in 1.5 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: 0.80
  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: 2.27

  Time building geometry restraints manager: 2.31 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:             0.920
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.090
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     24.280
  Find NCS groups from input model:        0.080
  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:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.640
-------------------------------------------------------------------------------
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  : 0.762 
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: 0.2011
  time to fit residues: 20.2434
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  : 0.763 
-------------------------------------------------------------------------------
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 = 0.3630 r_free = 0.3630 target = 0.079021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.057516 restraints weight = 33642.732|
|-----------------------------------------------------------------------------|
r_work (start): 0.3121 rms_B_bonded: 5.99
r_work (final): 0.3121
-------------------------------------------------------------------------------
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: 0.8003
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  : 0.869 
Fit side-chains
   revert: symmetry clash
REVERT: A  378 LEU cc_start: 0.9567 (OUTLIER) cc_final: 0.9365 (mm)
  outliers start: 14
  outliers final: 4
  residues processed: 59
  average time/residue: 0.1411
  time to fit residues: 13.0377
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  : 0.799 
-------------------------------------------------------------------------------
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:    0.0870
   chunk 13 optimal weight:    3.9990
   chunk 64 optimal weight:    0.6980
   chunk 1 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9990
   chunk 7 optimal weight:    8.9990
   chunk 38 optimal weight:   20.0000
   chunk 23 optimal weight:    0.7980
   chunk 75 optimal weight:    0.0170
   chunk 3 optimal weight:    9.9990
   overall best weight:    0.5198

-------------------------------------------------------------------------------
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 = 0.3644 r_free = 0.3644 target = 0.079577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.057144 restraints weight = 45137.965|
|-----------------------------------------------------------------------------|
r_work (start): 0.3115 rms_B_bonded: 6.95
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3117
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3117 r_free = 0.3117    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 = 0.3117 r_free = 0.3117    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3117
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.1777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7009  Z= 0.117
  Angle     :  0.658  10.637   9498  Z= 0.324
  Chirality :  0.043   0.159   1092
  Planarity :  0.005   0.045   1219
  Dihedral  :  4.967  41.802    946
  Min Nonbonded Distance : 2.007

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  7.36 %
    Favored  : 92.29 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 23.04 %
    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:  0.34 (0.30), residues: 857
  helix:  1.49 (0.26), residues: 403
  sheet: -0.61 (0.52), residues: 106
  loop : -0.98 (0.36), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 663 
 HIS   0.005   0.001   HIS A 984 
 PHE   0.011   0.001   PHE A 518 
 TYR   0.026   0.001   TYR A1009 
 ARG   0.006   0.000   ARG A 587 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03479 (  321)
  hydrogen bonds       : angle       4.20684 (  927)
  covalent geometry    : bond        0.00268 ( 7008)
  covalent geometry    : angle       0.65768 ( 9498)
  Misc. bond           : bond        0.00007 (    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
  59 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 47
  time to evaluate  : 0.770 
Fit side-chains
   revert: symmetry clash
REVERT: A  378 LEU cc_start: 0.9546 (OUTLIER) cc_final: 0.9339 (mp)
REVERT: A  645 MET cc_start: 0.9239 (mmm) cc_final: 0.8740 (mmm)
REVERT: A  871 MET cc_start: 0.8888 (ttp) cc_final: 0.8512 (tmm)
  outliers start: 12
  outliers final: 4
  residues processed: 56
  average time/residue: 0.1590
  time to fit residues: 13.2899
Evaluate side-chains
  46 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 41
  time to evaluate  : 0.871 
-------------------------------------------------------------------------------
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  665 LEU
Chi-restraints excluded: chain A residue  740 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 83 optimal weight:    5.9990
   chunk 39 optimal weight:    9.9990
   chunk 26 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 30 optimal weight:    7.9990
   chunk 21 optimal weight:    0.5980
   chunk 40 optimal weight:    5.9990
   chunk 51 optimal weight:    0.6980
   chunk 24 optimal weight:    0.8980
   chunk 63 optimal weight:    3.9990
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 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 = 0.3617 r_free = 0.3617 target = 0.078770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.059060 restraints weight = 28505.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.3142 rms_B_bonded: 5.67
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3140
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3140 r_free = 0.3140    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3140 r_free = 0.3140    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3140
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.2085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7009  Z= 0.126
  Angle     :  0.643  10.835   9498  Z= 0.316
  Chirality :  0.044   0.269   1092
  Planarity :  0.004   0.045   1219
  Dihedral  :  4.885  41.282    946
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  7.24 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 22.51 %
    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:  0.40 (0.30), residues: 857
  helix:  1.51 (0.26), residues: 409
  sheet: -0.48 (0.54), residues: 100
  loop : -1.00 (0.36), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 663 
 HIS   0.005   0.001   HIS A 984 
 PHE   0.015   0.001   PHE A 518 
 TYR   0.008   0.001   TYR A 619 
 ARG   0.003   0.000   ARG A 587 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03432 (  321)
  hydrogen bonds       : angle       4.07738 (  927)
  covalent geometry    : bond        0.00296 ( 7008)
  covalent geometry    : angle       0.64275 ( 9498)
  Misc. bond           : bond        0.00003 (    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: 16
    poor density    : 41
  time to evaluate  : 0.855 
Fit side-chains
   revert: symmetry clash
REVERT: A  645 MET cc_start: 0.9286 (mmm) cc_final: 0.8830 (mmm)
REVERT: A  844 ARG cc_start: 0.4678 (OUTLIER) cc_final: 0.4435 (mtm-85)
REVERT: A  942 MET cc_start: 0.9175 (ptp) cc_final: 0.8961 (ptp)
REVERT: A  965 GLN cc_start: 0.7411 (OUTLIER) cc_final: 0.6969 (mp10)
REVERT: A  973 GLN cc_start: 0.9394 (OUTLIER) cc_final: 0.9167 (mp10)
REVERT: A  981 MET cc_start: 0.8221 (mtp) cc_final: 0.7949 (mpp)
  outliers start: 16
  outliers final: 5
  residues processed: 55
  average time/residue: 0.1598
  time to fit residues: 13.2145
Evaluate side-chains
  45 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 37
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
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  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:    2.9990
   chunk 83 optimal weight:    3.9990
   chunk 5 optimal weight:   10.0000
   chunk 10 optimal weight:    6.9990
   chunk 46 optimal weight:    4.9990
   chunk 64 optimal weight:   10.0000
   chunk 11 optimal weight:    4.9990
   chunk 81 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   overall best weight:    2.7990

-------------------------------------------------------------------------------
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 818 HIS
** A 910 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 958 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.075018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.052709 restraints weight = 43233.951|
|-----------------------------------------------------------------------------|
r_work (start): 0.3002 rms_B_bonded: 6.60
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3004
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3004 r_free = 0.3004    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3004 r_free = 0.3004    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3004
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.2341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   7009  Z= 0.215
  Angle     :  0.716  10.192   9498  Z= 0.351
  Chirality :  0.046   0.232   1092
  Planarity :  0.004   0.043   1219
  Dihedral  :  5.091  39.747    946
  Min Nonbonded Distance : 1.872

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  7.83 %
    Favored  : 91.82 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 21.86 %
    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:  0.28 (0.30), residues: 857
  helix:  1.50 (0.26), residues: 405
  sheet: -0.55 (0.54), residues: 102
  loop : -1.14 (0.36), residues: 350

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   0.016   0.002   PHE A 518 
 TYR   0.011   0.001   TYR A 467 
 ARG   0.004   0.000   ARG A 773 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04060 (  321)
  hydrogen bonds       : angle       4.37658 (  927)
  covalent geometry    : bond        0.00504 ( 7008)
  covalent geometry    : angle       0.71593 ( 9498)
  Misc. bond           : bond        0.00041 (    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
  51 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 35
  time to evaluate  : 0.880 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  645 MET cc_start: 0.9309 (mmm) cc_final: 0.8858 (mmm)
REVERT: A  844 ARG cc_start: 0.5539 (OUTLIER) cc_final: 0.5126 (mtm-85)
REVERT: A  965 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.7313 (mt0)
REVERT: A  981 MET cc_start: 0.8444 (mtp) cc_final: 0.8137 (mpp)
  outliers start: 16
  outliers final: 10
  residues processed: 49
  average time/residue: 0.1642
  time to fit residues: 12.1575
Evaluate side-chains
  45 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 33
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
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  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
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:    7.9990
   chunk 63 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9990
   chunk 55 optimal weight:    0.0060
   chunk 64 optimal weight:    0.8980
   chunk 9 optimal weight:    0.7980
   chunk 76 optimal weight:    2.9990
   chunk 7 optimal weight:    7.9990
   chunk 66 optimal weight:    2.9990
   chunk 74 optimal weight:    0.0170
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.5034

-------------------------------------------------------------------------------
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 = 0.3600 r_free = 0.3600 target = 0.077656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.057186 restraints weight = 23346.304|
|-----------------------------------------------------------------------------|
r_work (start): 0.3107 rms_B_bonded: 5.04
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3107
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3107 r_free = 0.3107    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 = 0.3107 r_free = 0.3107    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3107
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.2427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7009  Z= 0.111
  Angle     :  0.648  10.258   9498  Z= 0.314
  Chirality :  0.043   0.221   1092
  Planarity :  0.004   0.045   1219
  Dihedral  :  4.914  38.677    946
  Min Nonbonded Distance : 2.039

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  7.36 %
    Favored  : 92.29 %
  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:  0.52 (0.30), residues: 857
  helix:  1.71 (0.26), residues: 404
  sheet: -0.44 (0.56), residues: 98
  loop : -1.03 (0.36), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 663 
 HIS   0.005   0.001   HIS A 984 
 PHE   0.012   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        0.03307 (  321)
  hydrogen bonds       : angle       4.01209 (  927)
  covalent geometry    : bond        0.00256 ( 7008)
  covalent geometry    : angle       0.64791 ( 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
  49 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 39
  time to evaluate  : 0.752 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  645 MET cc_start: 0.9291 (mmm) cc_final: 0.8819 (mmm)
REVERT: A  844 ARG cc_start: 0.5010 (OUTLIER) cc_final: 0.4712 (mtm-85)
REVERT: A  965 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.7297 (mt0)
REVERT: A  981 MET cc_start: 0.8285 (mtp) cc_final: 0.8083 (mpp)
  outliers start: 10
  outliers final: 7
  residues processed: 48
  average time/residue: 0.1654
  time to fit residues: 11.8938
Evaluate side-chains
  45 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 36
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 33 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9980
   chunk 21 optimal weight:    3.9990
   chunk 73 optimal weight:   10.0000
   chunk 80 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 61 optimal weight:    4.9990
   chunk 79 optimal weight:    0.5980
   chunk 81 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   overall best weight:    1.5186

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.076438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.053974 restraints weight = 42236.299|
|-----------------------------------------------------------------------------|
r_work (start): 0.3021 rms_B_bonded: 6.61
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3017
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3017 r_free = 0.3017    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3017 r_free = 0.3017    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3017
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.2586

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= 0.142
  Angle     :  0.653   9.810   9498  Z= 0.315
  Chirality :  0.044   0.206   1092
  Planarity :  0.004   0.043   1219
  Dihedral  :  4.888  40.090    946
  Min Nonbonded Distance : 1.967

Molprobity Statistics.
  All-atom Clashscore : 11.36
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  7.13 %
    Favored  : 92.52 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 22.91 %
    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:  0.49 (0.30), residues: 857
  helix:  1.66 (0.26), residues: 404
  sheet: -0.43 (0.55), residues: 98
  loop : -1.02 (0.36), residues: 355

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   0.018   0.001   PHE A 518 
 TYR   0.010   0.001   TYR A 619 
 ARG   0.003   0.000   ARG A 768 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03526 (  321)
  hydrogen bonds       : angle       4.08539 (  927)
  covalent geometry    : bond        0.00336 ( 7008)
  covalent geometry    : angle       0.65318 ( 9498)
  Misc. bond           : bond        0.00033 (    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
  48 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 34
  time to evaluate  : 0.768 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  645 MET cc_start: 0.9312 (mmm) cc_final: 0.8874 (mmm)
REVERT: A  734 ASP cc_start: 0.7417 (t0) cc_final: 0.7024 (t70)
REVERT: A  844 ARG cc_start: 0.5158 (OUTLIER) cc_final: 0.4832 (mtm-85)
REVERT: A  965 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.7316 (mt0)
REVERT: A  981 MET cc_start: 0.8293 (mtp) cc_final: 0.8066 (mpp)
  outliers start: 14
  outliers final: 7
  residues processed: 45
  average time/residue: 0.1660
  time to fit residues: 11.2767
Evaluate side-chains
  42 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 33
  time to evaluate  : 0.739 
-------------------------------------------------------------------------------
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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 32 optimal weight:    4.9990
   chunk 10 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 31 optimal weight:   10.0000
   chunk 61 optimal weight:    4.9990
   chunk 77 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0370
   chunk 42 optimal weight:    6.9990
   chunk 53 optimal weight:    2.9990
   chunk 67 optimal weight:    0.7980
   chunk 29 optimal weight:    5.9990
   overall best weight:    1.3062

-------------------------------------------------------------------------------
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 = 0.3580 r_free = 0.3580 target = 0.076537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.054102 restraints weight = 45839.349|
|-----------------------------------------------------------------------------|
r_work (start): 0.3024 rms_B_bonded: 6.84
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3021
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3021 r_free = 0.3021    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3021 r_free = 0.3021    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3021
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.2676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7009  Z= 0.132
  Angle     :  0.657   9.735   9498  Z= 0.315
  Chirality :  0.044   0.198   1092
  Planarity :  0.004   0.042   1219
  Dihedral  :  4.863  38.663    946
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 11.57
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  7.13 %
    Favored  : 92.52 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 23.04 %
    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:  0.52 (0.30), residues: 857
  helix:  1.68 (0.26), residues: 404
  sheet: -0.37 (0.56), residues: 98
  loop : -1.02 (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   0.016   0.001   PHE A 518 
 TYR   0.010   0.001   TYR A 619 
 ARG   0.003   0.000   ARG A 768 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03417 (  321)
  hydrogen bonds       : angle       4.05533 (  927)
  covalent geometry    : bond        0.00312 ( 7008)
  covalent geometry    : angle       0.65668 ( 9498)
  Misc. bond           : bond        0.00039 (    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
  45 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 34
  time to evaluate  : 0.807 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  645 MET cc_start: 0.9323 (mmm) cc_final: 0.8892 (mmm)
REVERT: A  734 ASP cc_start: 0.7436 (t0) cc_final: 0.7078 (t70)
REVERT: A  844 ARG cc_start: 0.5126 (OUTLIER) cc_final: 0.4800 (mtm-85)
REVERT: A  965 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.7300 (mt0)
  outliers start: 11
  outliers final: 8
  residues processed: 44
  average time/residue: 0.1718
  time to fit residues: 11.3205
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  : 0.827 
-------------------------------------------------------------------------------
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  665 LEU
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:    5.9990
   chunk 14 optimal weight:   10.0000
   chunk 67 optimal weight:    0.9990
   chunk 72 optimal weight:    0.0170
   chunk 5 optimal weight:   10.0000
   chunk 7 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 39 optimal weight:   10.0000
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.8024

-------------------------------------------------------------------------------
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 = 0.3600 r_free = 0.3600 target = 0.077535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.057067 restraints weight = 23368.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.3105 rms_B_bonded: 5.00
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3106
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3106 r_free = 0.3106    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3106 r_free = 0.3106    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3106
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.2811

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     :  0.665   9.710   9498  Z= 0.317
  Chirality :  0.043   0.202   1092
  Planarity :  0.004   0.043   1219
  Dihedral  :  4.865  39.009    946
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  7.36 %
    Favored  : 92.29 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 23.17 %
    Favored  : 75.39 %
  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:  0.60 (0.30), residues: 857
  helix:  1.67 (0.26), residues: 405
  sheet: -0.25 (0.54), residues: 106
  loop : -0.92 (0.37), residues: 346

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   0.015   0.001   PHE A 946 
 TYR   0.009   0.001   TYR A 619 
 ARG   0.003   0.000   ARG A 768 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03321 (  321)
  hydrogen bonds       : angle       4.00140 (  927)
  covalent geometry    : bond        0.00269 ( 7008)
  covalent geometry    : angle       0.66525 ( 9498)
  Misc. bond           : bond        0.00030 (    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
  42 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 33
  time to evaluate  : 0.895 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  645 MET cc_start: 0.9291 (mmm) cc_final: 0.8845 (mmm)
REVERT: A  734 ASP cc_start: 0.7418 (t0) cc_final: 0.7073 (t70)
REVERT: A  844 ARG cc_start: 0.5093 (OUTLIER) cc_final: 0.4811 (mtm-85)
REVERT: A  931 MET cc_start: 0.9042 (ptm) cc_final: 0.8514 (ppp)
REVERT: A  965 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7386 (mp10)
  outliers start: 9
  outliers final: 7
  residues processed: 41
  average time/residue: 0.1865
  time to fit residues: 11.4705
Evaluate side-chains
  42 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 33
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 1 optimal weight:    0.6980
   chunk 57 optimal weight:    0.7980
   chunk 16 optimal weight:    7.9990
   chunk 31 optimal weight:    9.9990
   chunk 5 optimal weight:    6.9990
   chunk 75 optimal weight:    0.0050
   chunk 34 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 85 optimal weight:    2.9990
   chunk 40 optimal weight:    8.9990
   overall best weight:    0.5994

-------------------------------------------------------------------------------
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 = 0.3609 r_free = 0.3609 target = 0.078014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.056894 restraints weight = 29813.099|
|-----------------------------------------------------------------------------|
r_work (start): 0.3098 rms_B_bonded: 5.68
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3100
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3100 r_free = 0.3100    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3100 r_free = 0.3100    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3100
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.2897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   7009  Z= 0.108
  Angle     :  0.642   9.735   9498  Z= 0.309
  Chirality :  0.043   0.198   1092
  Planarity :  0.004   0.045   1219
  Dihedral  :  4.787  39.425    946
  Min Nonbonded Distance : 2.026

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  7.01 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 23.04 %
    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:  0.69 (0.31), residues: 857
  helix:  1.76 (0.26), residues: 398
  sheet: -0.14 (0.55), residues: 106
  loop : -0.87 (0.37), residues: 353

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   0.015   0.001   PHE A 518 
 TYR   0.009   0.001   TYR A 619 
 ARG   0.003   0.000   ARG A 768 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03197 (  321)
  hydrogen bonds       : angle       4.00464 (  927)
  covalent geometry    : bond        0.00250 ( 7008)
  covalent geometry    : angle       0.64207 ( 9498)
  Misc. bond           : bond        0.00024 (    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
  46 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 35
  time to evaluate  : 0.801 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  645 MET cc_start: 0.9287 (mmm) cc_final: 0.8844 (mmm)
REVERT: A  844 ARG cc_start: 0.4999 (OUTLIER) cc_final: 0.4733 (mtm-85)
REVERT: A  965 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.7326 (mp10)
  outliers start: 11
  outliers final: 7
  residues processed: 45
  average time/residue: 0.1678
  time to fit residues: 11.3273
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  : 0.752 
-------------------------------------------------------------------------------
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 82 optimal weight:    2.9990
   chunk 81 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9980
   chunk 78 optimal weight:    0.7980
   chunk 44 optimal weight:    0.2980
   chunk 26 optimal weight:    5.9990
   chunk 71 optimal weight:    0.7980
   chunk 65 optimal weight:   10.0000
   chunk 80 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 3 optimal weight:    8.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 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 = 0.3621 r_free = 0.3621 target = 0.077750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.055729 restraints weight = 44950.980|
|-----------------------------------------------------------------------------|
r_work (start): 0.3092 rms_B_bonded: 6.71
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3094
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3094 r_free = 0.3094    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3094 r_free = 0.3094    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3094
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
moved from start:          0.2964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7009  Z= 0.109
  Angle     :  0.652   9.701   9498  Z= 0.311
  Chirality :  0.043   0.197   1092
  Planarity :  0.004   0.045   1219
  Dihedral  :  4.751  39.957    946
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  6.78 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 22.91 %
    Favored  : 75.39 %
  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:  0.73 (0.31), residues: 857
  helix:  1.78 (0.26), residues: 399
  sheet: -0.14 (0.55), residues: 108
  loop : -0.82 (0.37), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 932 
 HIS   0.006   0.001   HIS A 984 
 PHE   0.015   0.001   PHE A 518 
 TYR   0.009   0.001   TYR A 619 
 ARG   0.003   0.000   ARG A 768 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03149 (  321)
  hydrogen bonds       : angle       3.97822 (  927)
  covalent geometry    : bond        0.00255 ( 7008)
  covalent geometry    : angle       0.65229 ( 9498)
  Misc. bond           : bond        0.00028 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3862.07 seconds
wall clock time: 68 minutes 10.57 seconds (4090.57 seconds total)