Starting phenix.real_space_refine
on Wed Mar  4 09:25:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8b9j_15933/03_2026/8b9j_15933.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8b9j_15933/03_2026/8b9j_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8b9j_15933/03_2026/8b9j_15933.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8b9j_15933/03_2026/8b9j_15933.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8b9j_15933/03_2026/8b9j_15933.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8b9j_15933/03_2026/8b9j_15933.map"
  }
  resolution = 3.45
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 3.09, per 1000 atoms: 0.45
  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: 0.58
  Conformation dependent library (CDL) restraints added in 570.1 milliseconds
  

  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: 0.16
  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: 1.08

  Time building geometry restraints manager: 0.73 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:             1.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.700
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.460
-------------------------------------------------------------------------------
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 : 13.67
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.013   0.001   ARG A 938 
 TYR   0.009   0.001   TYR A 550 
 PHE   0.031   0.002   PHE A 672 
 TRP   0.020   0.002   TRP A 949 
 HIS   0.003   0.001   HIS A 941 

Details of bonding type rmsd
  covalent geometry    : bond        0.00481 ( 7008)
  covalent geometry    : angle       1.36541 ( 9498)
  hydrogen bonds       : bond        0.14376 (  321)
  hydrogen bonds       : angle       5.67369 (  927)
  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  : 0.227 
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: 0.0844
  time to fit residues: 8.5062
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  : 0.197 
-------------------------------------------------------------------------------
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 49 optimal weight:    5.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    8.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:   10.0000
   chunk 45 optimal weight:    8.9990
   chunk 74 optimal weight:    0.5980
   overall best weight:    1.8586

-------------------------------------------------------------------------------
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 = 0.3586 r_free = 0.3586 target = 0.076703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.054355 restraints weight = 45637.316|
|-----------------------------------------------------------------------------|
r_work (start): 0.3044 rms_B_bonded: 6.82
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3040
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3040 r_free = 0.3040    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3040 r_free = 0.3040    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3040
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.1443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   7009  Z= 0.175
  Angle     :  0.732   7.790   9498  Z= 0.363
  Chirality :  0.045   0.148   1092
  Planarity :  0.005   0.055   1219
  Dihedral  :  5.990  51.256    955
  Min Nonbonded Distance : 1.923

Molprobity Statistics.
  All-atom Clashscore : 12.58
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  8.06 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 24.74 %
    Favored  : 73.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.07 (0.30), residues: 857
  helix:  1.17 (0.25), residues: 403
  sheet: -1.03 (0.54), residues: 98
  loop : -1.14 (0.36), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 590 
 TYR   0.016   0.001   TYR A1009 
 PHE   0.020   0.002   PHE A 518 
 TRP   0.014   0.002   TRP A 949 
 HIS   0.005   0.001   HIS A 984 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 7008)
  covalent geometry    : angle       0.73207 ( 9498)
  hydrogen bonds       : bond        0.04148 (  321)
  hydrogen bonds       : angle       4.58383 (  927)
  Misc. bond           : bond        0.00205 (    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
  54 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 41
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  378 LEU cc_start: 0.9554 (OUTLIER) cc_final: 0.9337 (mm)
  outliers start: 13
  outliers final: 4
  residues processed: 53
  average time/residue: 0.0607
  time to fit residues: 5.1550
Evaluate side-chains
  43 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 38
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
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 32 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9990
   chunk 56 optimal weight:    5.9990
   chunk 20 optimal weight:    0.7980
   chunk 27 optimal weight:    3.9990
   chunk 30 optimal weight:   10.0000
   chunk 82 optimal weight:    5.9990
   chunk 28 optimal weight:    1.9990
   chunk 69 optimal weight:    0.0030
   chunk 84 optimal weight:    0.9980
   chunk 2 optimal weight:    9.9990
   overall best weight:    0.9594

-------------------------------------------------------------------------------
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 = 0.3669 r_free = 0.3669 target = 0.078418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.056699 restraints weight = 42101.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.3167 rms_B_bonded: 6.36
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3167
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3167 r_free = 0.3167    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3167 r_free = 0.3167    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3167
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.1788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7009  Z= 0.127
  Angle     :  0.656   7.561   9498  Z= 0.324
  Chirality :  0.043   0.154   1092
  Planarity :  0.005   0.047   1219
  Dihedral  :  5.013  40.638    946
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  7.36 %
    Favored  : 92.29 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 22.91 %
    Favored  : 74.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.32 (0.30), residues: 857
  helix:  1.59 (0.26), residues: 397
  sheet: -0.81 (0.52), residues: 106
  loop : -1.03 (0.36), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 587 
 TYR   0.031   0.001   TYR A1009 
 PHE   0.012   0.001   PHE A 518 
 TRP   0.012   0.001   TRP A 949 
 HIS   0.005   0.001   HIS A 984 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 7008)
  covalent geometry    : angle       0.65595 ( 9498)
  hydrogen bonds       : bond        0.03590 (  321)
  hydrogen bonds       : angle       4.27452 (  927)
  Misc. bond           : bond        0.00003 (    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
  61 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 43
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
REVERT: A  378 LEU cc_start: 0.9583 (OUTLIER) cc_final: 0.9361 (mm)
REVERT: A  645 MET cc_start: 0.9178 (mmm) cc_final: 0.8680 (mmm)
REVERT: A  844 ARG cc_start: 0.5112 (OUTLIER) cc_final: 0.4841 (mtm-85)
  outliers start: 18
  outliers final: 7
  residues processed: 58
  average time/residue: 0.0667
  time to fit residues: 5.9144
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  : 0.269 
-------------------------------------------------------------------------------
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  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  919 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 79 optimal weight:    9.9990
   chunk 31 optimal weight:    9.9990
   chunk 64 optimal weight:   10.0000
   chunk 2 optimal weight:   10.0000
   chunk 10 optimal weight:    5.9990
   chunk 80 optimal weight:    1.9990
   chunk 71 optimal weight:    0.4980
   chunk 78 optimal weight:    5.9990
   chunk 68 optimal weight:    5.9990
   chunk 54 optimal weight:    8.9990
   overall best weight:    3.2988

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.073888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.051747 restraints weight = 43217.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.2980 rms_B_bonded: 6.54
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2981
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2981 r_free = 0.2981    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2981 r_free = 0.2981    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2981
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.2321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   7009  Z= 0.245
  Angle     :  0.734   9.724   9498  Z= 0.363
  Chirality :  0.046   0.220   1092
  Planarity :  0.005   0.042   1219
  Dihedral  :  5.254  41.701    946
  Min Nonbonded Distance : 1.865

Molprobity Statistics.
  All-atom Clashscore : 13.24
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  7.94 %
    Favored  : 91.71 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 21.20 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.10 (0.30), residues: 857
  helix:  1.34 (0.26), residues: 406
  sheet: -0.81 (0.53), residues: 102
  loop : -1.17 (0.36), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 587 
 TYR   0.013   0.002   TYR A1009 
 PHE   0.016   0.002   PHE A 659 
 TRP   0.010   0.001   TRP A 932 
 HIS   0.005   0.001   HIS A 941 

Details of bonding type rmsd
  covalent geometry    : bond        0.00572 ( 7008)
  covalent geometry    : angle       0.73372 ( 9498)
  hydrogen bonds       : bond        0.04317 (  321)
  hydrogen bonds       : angle       4.61606 (  927)
  Misc. bond           : bond        0.00053 (    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
  59 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 37
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  645 MET cc_start: 0.9296 (mmm) cc_final: 0.8813 (mmm)
REVERT: A  734 ASP cc_start: 0.7823 (t0) cc_final: 0.7424 (t70)
REVERT: A  844 ARG cc_start: 0.5653 (OUTLIER) cc_final: 0.5247 (mtm-85)
REVERT: A  855 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8634 (mp)
REVERT: A  965 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7247 (mt0)
  outliers start: 22
  outliers final: 9
  residues processed: 55
  average time/residue: 0.0791
  time to fit residues: 6.2638
Evaluate side-chains
  47 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 35
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
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  855 LEU
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 3 optimal weight:    0.0980
   chunk 49 optimal weight:    6.9990
   chunk 32 optimal weight:    4.9990
   chunk 30 optimal weight:    9.9990
   chunk 41 optimal weight:    7.9990
   chunk 60 optimal weight:   10.0000
   chunk 21 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 27 optimal weight:    0.6980
   chunk 2 optimal weight:    5.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 = 0.3585 r_free = 0.3585 target = 0.076319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.055974 restraints weight = 30276.700|
|-----------------------------------------------------------------------------|
r_work (start): 0.3100 rms_B_bonded: 5.39
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3101
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3101 r_free = 0.3101    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3101 r_free = 0.3101    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3101
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
moved from start:          0.2444

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= 0.127
  Angle     :  0.656   9.431   9498  Z= 0.322
  Chirality :  0.044   0.239   1092
  Planarity :  0.004   0.045   1219
  Dihedral  :  5.060  39.824    946
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  7.24 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 22.25 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.45 (0.30), residues: 857
  helix:  1.69 (0.26), residues: 404
  sheet: -0.64 (0.55), residues: 98
  loop : -1.06 (0.36), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A1131 
 TYR   0.008   0.001   TYR A 619 
 PHE   0.010   0.001   PHE A 672 
 TRP   0.010   0.001   TRP A 949 
 HIS   0.004   0.001   HIS A 984 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 7008)
  covalent geometry    : angle       0.65560 ( 9498)
  hydrogen bonds       : bond        0.03511 (  321)
  hydrogen bonds       : angle       4.13761 (  927)
  Misc. bond           : bond        0.00034 (    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
  49 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 33
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  645 MET cc_start: 0.9271 (mmm) cc_final: 0.8796 (mmm)
REVERT: A  844 ARG cc_start: 0.5259 (OUTLIER) cc_final: 0.4899 (mtm-85)
REVERT: A  965 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7211 (mt0)
REVERT: A  981 MET cc_start: 0.8338 (mtp) cc_final: 0.8073 (mpp)
REVERT: A 1003 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8390 (mp)
  outliers start: 16
  outliers final: 10
  residues processed: 47
  average time/residue: 0.0673
  time to fit residues: 4.7633
Evaluate side-chains
  46 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 33
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
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  690 CYS
Chi-restraints excluded: chain A residue  740 MET
Chi-restraints excluded: chain A residue  762 LEU
Chi-restraints excluded: chain A residue  844 ARG
Chi-restraints excluded: chain A residue  919 CYS
Chi-restraints excluded: chain A residue  965 GLN
Chi-restraints excluded: chain A residue  973 GLN
Chi-restraints excluded: chain A residue 1003 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 40 optimal weight:   10.0000
   chunk 39 optimal weight:    5.9990
   chunk 57 optimal weight:    0.6980
   chunk 56 optimal weight:    0.0060
   chunk 34 optimal weight:    4.9990
   chunk 78 optimal weight:    9.9990
   chunk 43 optimal weight:    0.9980
   chunk 81 optimal weight:    6.9990
   chunk 24 optimal weight:    3.9990
   chunk 63 optimal weight:    5.9990
   chunk 47 optimal weight:    0.7980
   overall best weight:    1.2998

-------------------------------------------------------------------------------
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 = 0.3573 r_free = 0.3573 target = 0.076176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.054903 restraints weight = 29971.753|
|-----------------------------------------------------------------------------|
r_work (start): 0.3049 rms_B_bonded: 5.61
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3047
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3047 r_free = 0.3047    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3047 r_free = 0.3047    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3047
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.2551

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= 0.133
  Angle     :  0.654  11.502   9498  Z= 0.318
  Chirality :  0.044   0.222   1092
  Planarity :  0.004   0.043   1219
  Dihedral  :  5.019  41.429    946
  Min Nonbonded Distance : 1.982

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  6.78 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 22.25 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.49 (0.30), residues: 857
  helix:  1.72 (0.26), residues: 405
  sheet: -0.66 (0.54), residues: 98
  loop : -1.03 (0.36), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1131 
 TYR   0.008   0.001   TYR A 619 
 PHE   0.013   0.001   PHE A 518 
 TRP   0.008   0.001   TRP A 932 
 HIS   0.005   0.001   HIS A 984 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 7008)
  covalent geometry    : angle       0.65429 ( 9498)
  hydrogen bonds       : bond        0.03585 (  321)
  hydrogen bonds       : angle       4.11089 (  927)
  Misc. bond           : bond        0.00032 (    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: 17
    poor density    : 34
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  645 MET cc_start: 0.9299 (mmm) cc_final: 0.8852 (mmm)
REVERT: A  844 ARG cc_start: 0.5117 (OUTLIER) cc_final: 0.4784 (mtm-85)
REVERT: A  871 MET cc_start: 0.8781 (ttp) cc_final: 0.8432 (tmm)
REVERT: A  957 MET cc_start: 0.8691 (mmp) cc_final: 0.8468 (mmp)
REVERT: A  965 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.7234 (mt0)
REVERT: A  981 MET cc_start: 0.8320 (mtp) cc_final: 0.8059 (mpp)
  outliers start: 17
  outliers final: 8
  residues processed: 49
  average time/residue: 0.0692
  time to fit residues: 5.0550
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  : 0.270 
-------------------------------------------------------------------------------
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  762 LEU
Chi-restraints excluded: chain A residue  797 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 21 optimal weight:    0.0370
   chunk 2 optimal weight:    5.9990
   chunk 36 optimal weight:    6.9990
   chunk 55 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   chunk 3 optimal weight:    6.9990
   chunk 43 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   overall best weight:    0.7262

-------------------------------------------------------------------------------
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 958 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.077086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.056682 restraints weight = 23316.092|
|-----------------------------------------------------------------------------|
r_work (start): 0.3100 rms_B_bonded: 4.95
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3103
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3103 r_free = 0.3103    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 = 0.3103 r_free = 0.3103    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3103
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.2719

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     :  0.644  10.861   9498  Z= 0.312
  Chirality :  0.043   0.220   1092
  Planarity :  0.004   0.043   1219
  Dihedral  :  4.910  39.653    946
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  7.36 %
    Favored  : 92.29 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 22.77 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.64 (0.31), residues: 857
  helix:  1.80 (0.26), residues: 405
  sheet: -0.42 (0.55), residues: 98
  loop : -0.95 (0.36), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1131 
 TYR   0.007   0.001   TYR A 619 
 PHE   0.010   0.001   PHE A 946 
 TRP   0.009   0.001   TRP A 932 
 HIS   0.005   0.001   HIS A 984 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 7008)
  covalent geometry    : angle       0.64410 ( 9498)
  hydrogen bonds       : bond        0.03279 (  321)
  hydrogen bonds       : angle       3.99138 (  927)
  Misc. bond           : bond        0.00022 (    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  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  645 MET cc_start: 0.9290 (mmm) cc_final: 0.8835 (mmm)
REVERT: A  844 ARG cc_start: 0.4952 (OUTLIER) cc_final: 0.4688 (mtm-85)
REVERT: A  871 MET cc_start: 0.8706 (ttp) cc_final: 0.8416 (tmm)
REVERT: A  957 MET cc_start: 0.8643 (mmp) cc_final: 0.8440 (mmp)
REVERT: A  965 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.7307 (mp10)
REVERT: A  981 MET cc_start: 0.8270 (mtp) cc_final: 0.8068 (mpp)
  outliers start: 13
  outliers final: 9
  residues processed: 45
  average time/residue: 0.0709
  time to fit residues: 4.8564
Evaluate side-chains
  42 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 31
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
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  844 ARG
Chi-restraints excluded: chain A residue  919 CYS
Chi-restraints excluded: chain A residue  965 GLN
Chi-restraints excluded: chain A residue  973 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 78 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9980
   chunk 72 optimal weight:    0.0270
   chunk 36 optimal weight:    6.9990
   chunk 71 optimal weight:    5.9990
   chunk 7 optimal weight:    9.9990
   chunk 35 optimal weight:    9.9990
   chunk 48 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9990
   overall best weight:    1.2044

-------------------------------------------------------------------------------
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 = 0.3579 r_free = 0.3579 target = 0.076466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.054795 restraints weight = 33558.920|
|-----------------------------------------------------------------------------|
r_work (start): 0.3048 rms_B_bonded: 5.93
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3047
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3047 r_free = 0.3047    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3047 r_free = 0.3047    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3047
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.2801

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= 0.127
  Angle     :  0.650  10.533   9498  Z= 0.314
  Chirality :  0.043   0.209   1092
  Planarity :  0.004   0.044   1219
  Dihedral  :  4.906  39.745    946
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  6.89 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 22.77 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.65 (0.31), residues: 857
  helix:  1.71 (0.26), residues: 410
  sheet: -0.42 (0.55), residues: 98
  loop : -0.85 (0.36), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1131 
 TYR   0.010   0.001   TYR A 619 
 PHE   0.013   0.001   PHE A 946 
 TRP   0.009   0.001   TRP A 932 
 HIS   0.005   0.001   HIS A 984 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 7008)
  covalent geometry    : angle       0.64968 ( 9498)
  hydrogen bonds       : bond        0.03380 (  321)
  hydrogen bonds       : angle       4.04368 (  927)
  Misc. bond           : bond        0.00030 (    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: 12
    poor density    : 33
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  645 MET cc_start: 0.9307 (mmm) cc_final: 0.8861 (mmm)
REVERT: A  734 ASP cc_start: 0.7331 (t0) cc_final: 0.6975 (t70)
REVERT: A  844 ARG cc_start: 0.5059 (OUTLIER) cc_final: 0.4771 (mtm-85)
REVERT: A  871 MET cc_start: 0.8778 (ttp) cc_final: 0.8452 (tmm)
REVERT: A  965 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.7265 (mp10)
REVERT: A  981 MET cc_start: 0.8266 (mtp) cc_final: 0.8060 (mpp)
  outliers start: 12
  outliers final: 8
  residues processed: 43
  average time/residue: 0.0769
  time to fit residues: 4.7744
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  : 0.201 
-------------------------------------------------------------------------------
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  690 CYS
Chi-restraints excluded: chain A residue  844 ARG
Chi-restraints excluded: chain A residue  919 CYS
Chi-restraints excluded: chain A residue  965 GLN
Chi-restraints excluded: chain A residue  973 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 22 optimal weight:    0.7980
   chunk 28 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 8 optimal weight:    8.9990
   chunk 80 optimal weight:    0.1980
   chunk 26 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 65 optimal weight:    9.9990
   chunk 69 optimal weight:    5.9990
   chunk 66 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.9986

-------------------------------------------------------------------------------
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 = 0.3586 r_free = 0.3586 target = 0.076833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.054422 restraints weight = 46219.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.3033 rms_B_bonded: 6.97
r_work (final): 0.3033
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3034
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3034 r_free = 0.3034    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3034 r_free = 0.3034    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3034
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.2911

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= 0.118
  Angle     :  0.646  10.415   9498  Z= 0.312
  Chirality :  0.043   0.211   1092
  Planarity :  0.004   0.044   1219
  Dihedral  :  4.851  39.374    946
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  7.36 %
    Favored  : 92.29 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 23.04 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.77 (0.31), residues: 857
  helix:  1.81 (0.26), residues: 404
  sheet: -0.30 (0.55), residues: 98
  loop : -0.76 (0.36), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1131 
 TYR   0.010   0.001   TYR A 619 
 PHE   0.015   0.001   PHE A 518 
 TRP   0.010   0.001   TRP A 932 
 HIS   0.005   0.001   HIS A 984 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 7008)
  covalent geometry    : angle       0.64633 ( 9498)
  hydrogen bonds       : bond        0.03256 (  321)
  hydrogen bonds       : angle       3.99541 (  927)
  Misc. bond           : bond        0.00036 (    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
  43 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 33
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  645 MET cc_start: 0.9324 (mmm) cc_final: 0.8895 (mmm)
REVERT: A  734 ASP cc_start: 0.7366 (t0) cc_final: 0.7025 (t70)
REVERT: A  844 ARG cc_start: 0.4962 (OUTLIER) cc_final: 0.4701 (mtm-85)
REVERT: A  871 MET cc_start: 0.8698 (ttp) cc_final: 0.8385 (tmm)
REVERT: A  965 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.7320 (mp10)
  outliers start: 10
  outliers final: 7
  residues processed: 42
  average time/residue: 0.0747
  time to fit residues: 4.7305
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  : 0.263 
-------------------------------------------------------------------------------
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  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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 18 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9990
   chunk 62 optimal weight:    4.9990
   chunk 30 optimal weight:    0.0870
   chunk 70 optimal weight:    1.9990
   chunk 77 optimal weight:    0.5980
   chunk 60 optimal weight:    0.0870
   chunk 34 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.5136

-------------------------------------------------------------------------------
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 = 0.3607 r_free = 0.3607 target = 0.077077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.056545 restraints weight = 29496.378|
|-----------------------------------------------------------------------------|
r_work (start): 0.3118 rms_B_bonded: 5.46
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3119
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3119 r_free = 0.3119    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3119 r_free = 0.3119    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3119
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.2999

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     :  0.653  10.450   9498  Z= 0.314
  Chirality :  0.043   0.207   1092
  Planarity :  0.004   0.044   1219
  Dihedral  :  4.871  39.706    946
  Min Nonbonded Distance : 2.032

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  7.01 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 23.43 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.80 (0.31), residues: 857
  helix:  1.79 (0.26), residues: 404
  sheet: -0.20 (0.56), residues: 98
  loop : -0.71 (0.37), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1131 
 TYR   0.009   0.001   TYR A 619 
 PHE   0.013   0.001   PHE A 946 
 TRP   0.009   0.001   TRP A 932 
 HIS   0.006   0.001   HIS A 984 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 7008)
  covalent geometry    : angle       0.65330 ( 9498)
  hydrogen bonds       : bond        0.03222 (  321)
  hydrogen bonds       : angle       3.97419 (  927)
  Misc. bond           : bond        0.00018 (    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  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  358 MET cc_start: 0.9312 (mmm) cc_final: 0.9015 (mmm)
REVERT: A  645 MET cc_start: 0.9256 (mmm) cc_final: 0.8814 (mmm)
REVERT: A  844 ARG cc_start: 0.5032 (OUTLIER) cc_final: 0.4794 (mtm-85)
REVERT: A  871 MET cc_start: 0.8862 (ttp) cc_final: 0.8539 (tmm)
REVERT: A  942 MET cc_start: 0.9268 (pmm) cc_final: 0.9033 (pmm)
REVERT: A  965 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7400 (mp10)
  outliers start: 10
  outliers final: 7
  residues processed: 43
  average time/residue: 0.0789
  time to fit residues: 5.0331
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  : 0.290 
-------------------------------------------------------------------------------
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0050
   chunk 68 optimal weight:    3.9990
   chunk 2 optimal weight:    9.9990
   chunk 40 optimal weight:    0.0040
   chunk 29 optimal weight:    5.9990
   chunk 69 optimal weight:    0.9990
   chunk 67 optimal weight:    0.7980
   chunk 85 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.7610

-------------------------------------------------------------------------------
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 = 0.3608 r_free = 0.3608 target = 0.077087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.054892 restraints weight = 54529.816|
|-----------------------------------------------------------------------------|
r_work (start): 0.3072 rms_B_bonded: 7.34
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3075
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3075 r_free = 0.3075    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3075 r_free = 0.3075    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3075
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.3061

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= 0.110
  Angle     :  0.641  10.392   9498  Z= 0.308
  Chirality :  0.043   0.205   1092
  Planarity :  0.004   0.044   1219
  Dihedral  :  4.769  40.251    946
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  6.89 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 23.30 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.83 (0.31), residues: 857
  helix:  1.81 (0.26), residues: 404
  sheet: -0.17 (0.56), residues: 98
  loop : -0.70 (0.37), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1131 
 TYR   0.009   0.001   TYR A 619 
 PHE   0.017   0.001   PHE A 518 
 TRP   0.010   0.001   TRP A 932 
 HIS   0.005   0.001   HIS A 984 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 7008)
  covalent geometry    : angle       0.64125 ( 9498)
  hydrogen bonds       : bond        0.03138 (  321)
  hydrogen bonds       : angle       3.92623 (  927)
  Misc. bond           : bond        0.00020 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1631.34 seconds
wall clock time: 28 minutes 38.22 seconds (1718.22 seconds total)