Starting phenix.real_space_refine
on Sun Apr  5 18:25:59 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7jl0_22368/04_2026/7jl0_22368.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7jl0_22368/04_2026/7jl0_22368.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7jl0_22368/04_2026/7jl0_22368.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7jl0_22368/04_2026/7jl0_22368.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7jl0_22368/04_2026/7jl0_22368.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7jl0_22368/04_2026/7jl0_22368.map"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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 5893 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: 9
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     Al      1      5.89       5
     P      30      5.49       5
     Mg      1      5.21       5
     S      42      5.16       5
     C    4554      2.51       5
     N    1283      2.21       5
     O    1438      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 35 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7354
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "X"
      Number of atoms: 300
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 300
          Classifications: {'RNA': 14}
          Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 6}
          Link IDs: {'rna3p': 13}
    Chain: "Y"
      Number of atoms: 295
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 295
          Classifications: {'RNA': 14}
          Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 8}
          Link IDs: {'rna3p': 13}
    Chain: "A"
      Number of atoms: 5311
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 662, 5311
          Classifications: {'peptide': 662}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 21, 'TRANS': 640}
          Chain breaks: 8
          Unresolved non-hydrogen bonds: 35
          Unresolved non-hydrogen angles: 40
          Unresolved non-hydrogen dihedrals: 33
          Planarities with less than four sites: {'GLU:plan': 2, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "B"
      Number of atoms: 1414
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 180, 1404
          Classifications: {'peptide': 180}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 167}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 55
          Unresolved non-hydrogen angles: 66
          Unresolved non-hydrogen dihedrals: 44
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 5, 'GLN:plan1': 3, 'ASP:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 43
      Conformer: "B"
        Number of residues, atoms: 180, 1404
          Classifications: {'peptide': 180}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 167}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 55
          Unresolved non-hydrogen angles: 66
          Unresolved non-hydrogen dihedrals: 44
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 5, 'GLN:plan1': 3, 'ASP:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 43
          bond proxies already assigned to first conformer: 1438
    Chain: "A"
      Number of atoms: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 34
          Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1, 'ALF': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   5098  SG  CYS A 907      86.171  20.420  28.789  1.00 67.24           S
  ATOM   5121  SG  CYS A 910      86.717  17.188  28.952  1.00 79.54           S
  ATOM   5454  SG  CYS A 962      86.167  18.607  25.327  1.00 82.04           S
  ATOM   5469  SG  CYS A 964      83.656  17.332  28.245  1.00 96.45           S

  Time building chain proxies: 1.97, per 1000 atoms: 0.27
  Number of scatterers: 7354
  At special positions: 0
  Unit cell: (114.989, 102.558, 71.4799, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 9
    Type Number    sf(0)
     Zn      1     29.99
     S      42     16.00
     P      30     15.00
     Al      1     13.00
     Mg      1     11.99
     F       4      9.00
     O    1438      8.00
     N    1283      7.00
     C    4554      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=0, symmetry=0
  Time building additional restraints: 0.62
  Conformation dependent library (CDL) restraints added in 233.3 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1101 "
        pdb="ZN    ZN A1101 " - pdb=" SG  CYS A 910 "
        pdb="ZN    ZN A1101 " - pdb=" SG  CYS A 907 "
        pdb="ZN    ZN A1101 " - pdb=" SG  CYS A 964 "
        pdb="ZN    ZN A1101 " - pdb=" SG  CYS A 962 "
      Number of angles added : 6


  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1602

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 7 sheets defined
      43.0% alpha, 15.1% beta
      10 base pairs and 18 stacking pairs defined.
    Time for finding SS restraints: 0.82
  Creating SS restraints...
    Processing helix  chain 'A' and resid 309 through 317
    Processing helix  chain 'A' and resid 318 through 321
      removed outlier: 3.667A  pdb=" N   GLU A 321 " --> pdb=" O   PRO A 318 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 318 through 321'
    Processing helix  chain 'A' and resid 334 through 353
      removed outlier: 3.672A  pdb=" N   ALA A 353 " --> pdb=" O   LYS A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 375
      removed outlier: 3.584A  pdb=" N   VAL A 369 " --> pdb=" O   LYS A 365 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   GLU A 370 " --> pdb=" O   VAL A 366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 381
      removed outlier: 3.718A  pdb=" N   PHE A 380 " --> pdb=" O   GLU A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 407
    Processing helix  chain 'A' and resid 414 through 422
    Processing helix  chain 'A' and resid 445 through 448
    Processing helix  chain 'A' and resid 452 through 472
      removed outlier: 3.668A  pdb=" N   ASN A 456 " --> pdb=" O   ALA A 452 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   ILE A 457 " --> pdb=" O   VAL A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 514
    Processing helix  chain 'A' and resid 524 through 532
    Processing helix  chain 'A' and resid 548 through 566
      removed outlier: 4.626A  pdb=" N   GLU A 552 " --> pdb=" O   ASP A 548 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ILE A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   CYS A 565 " --> pdb=" O   ILE A 561 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 575 through 593
      removed outlier: 3.725A  pdb=" N   GLU A 579 " --> pdb=" O   THR A 575 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 597 through 617
    Processing helix  chain 'A' and resid 618 through 640
      removed outlier: 3.812A  pdb=" N   ALA A 622 " --> pdb=" O   ARG A 618 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   GLU A 632 " --> pdb=" O   THR A 628 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ALA A 639 " --> pdb=" O   ASP A 635 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   VAL A 640 " --> pdb=" O   LYS A 636 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 673 through 692
      removed outlier: 4.114A  pdb=" N   MET A 677 " --> pdb=" O   ASP A 673 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   LEU A 679 " --> pdb=" O   PHE A 675 " (cutoff:3.500A)
      removed outlier: 4.830A  pdb=" N   GLU A 682 " --> pdb=" O   THR A 678 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 699 through 716
      removed outlier: 3.687A  pdb=" N   LYS A 703 " --> pdb=" O   GLU A 699 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   GLU A 716 " --> pdb=" O   TYR A 712 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 727 through 741
      removed outlier: 4.069A  pdb=" N   ASN A 741 " --> pdb=" O   TRP A 737 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 742 through 747
      removed outlier: 3.881A  pdb=" N   GLU A 746 " --> pdb=" O   GLU A 742 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   VAL A 747 " --> pdb=" O   LYS A 743 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 742 through 747'
    Processing helix  chain 'A' and resid 767 through 781
      removed outlier: 3.861A  pdb=" N   THR A 780 " --> pdb=" O   SER A 776 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   GLY A 781 " --> pdb=" O   LYS A 777 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 790 through 793
    Processing helix  chain 'A' and resid 813 through 822
      removed outlier: 4.360A  pdb=" N   ALA A 819 " --> pdb=" O   ALA A 815 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ARG A 820 " --> pdb=" O   MET A 816 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   GLY A 821 " --> pdb=" O   VAL A 817 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 840 through 862
    Processing helix  chain 'A' and resid 865 through 895
      removed outlier: 3.617A  pdb=" N   ILE A 881 " --> pdb=" O   GLN A 877 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 933 through 939
      removed outlier: 4.151A  pdb=" N   TYR A 939 " --> pdb=" O   PHE A 935 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 983 through 985
      No H-bonds generated for 'chain 'A' and resid 983 through 985'
    Processing helix  chain 'B' and resid 322 through 327
    Processing helix  chain 'B' and resid 328 through 330
      No H-bonds generated for 'chain 'B' and resid 328 through 330'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 325 through 328
      removed outlier: 7.083A  pdb=" N   ILE A 325 " --> pdb=" O   GLY A 486 " (cutoff:3.500A)
      removed outlier: 8.720A  pdb=" N   THR A 488 " --> pdb=" O   ILE A 325 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   ILE A 327 " --> pdb=" O   THR A 488 " (cutoff:3.500A)
      removed outlier: 6.064A  pdb=" N   ILE A 440 " --> pdb=" O   LEU A 485 " (cutoff:3.500A)
      removed outlier: 7.729A  pdb=" N   LEU A 487 " --> pdb=" O   ILE A 440 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   ILE A 442 " --> pdb=" O   LEU A 487 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 536 through 541
      removed outlier: 3.656A  pdb=" N   ALA A 834 " --> pdb=" O   ALA A 540 " (cutoff:3.500A)
      removed outlier: 6.324A  pdb=" N   GLY A 721 " --> pdb=" O   LEU A 786 " (cutoff:3.500A)
      removed outlier: 7.438A  pdb=" N   ALA A 788 " --> pdb=" O   GLY A 721 " (cutoff:3.500A)
      removed outlier: 6.013A  pdb=" N   ILE A 723 " --> pdb=" O   ALA A 788 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   HIS A 752 " --> pdb=" O   LEU A 785 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 913 through 916
      removed outlier: 6.903A  pdb=" N   LEU A 913 " --> pdb=" O   CYS A 907 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   CYS A 907 " --> pdb=" O   LEU A 913 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   CYS A 915 " --> pdb=" O   PHE A 905 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 920 through 923
    Processing sheet with id=AA5, first strand: chain 'A' and resid 940 through 942
      removed outlier: 4.532A  pdb=" N   GLY A 969 " --> pdb=" O   ILE A 960 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   LEU A 979 " --> pdb=" O   MET A 972 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 344 through 347
      removed outlier: 3.934A  pdb=" N   TYR B 475 " --> pdb=" O   PHE B 464 " (cutoff:3.500A)
      removed outlier: 7.141A  pdb=" N   SER B 466 " --> pdb=" O   PRO B 473 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 372 through 374

    309 hydrogen bonds defined for protein.
    886 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      25 hydrogen bonds
      50 hydrogen bond angles
      0 basepair planarities
      10 basepair parallelities
      18 stacking parallelities
  Total time for adding SS restraints: 1.32

  Time building geometry restraints manager: 0.78 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: 1806
        1.33 -     1.45: 1678
        1.45 -     1.58: 3941
        1.58 -     1.70: 58
        1.70 -     1.82: 69
  Bond restraints: 7552
  Sorted by residual:
  bond pdb=" CA  LYS A 782 "
       pdb=" C   LYS A 782 "
    ideal  model  delta    sigma   weight residual
    1.521  1.601 -0.079 1.29e-02 6.01e+03 3.79e+01
  bond pdb=" F1  ALF A1103 "
       pdb="AL   ALF A1103 "
    ideal  model  delta    sigma   weight residual
    1.684  1.780 -0.096 2.00e-02 2.50e+03 2.30e+01
  bond pdb=" F3  ALF A1103 "
       pdb="AL   ALF A1103 "
    ideal  model  delta    sigma   weight residual
    1.685  1.780 -0.095 2.00e-02 2.50e+03 2.24e+01
  bond pdb=" F4  ALF A1103 "
       pdb="AL   ALF A1103 "
    ideal  model  delta    sigma   weight residual
    1.686  1.780 -0.094 2.00e-02 2.50e+03 2.21e+01
  bond pdb=" F2  ALF A1103 "
       pdb="AL   ALF A1103 "
    ideal  model  delta    sigma   weight residual
    1.685  1.778 -0.093 2.00e-02 2.50e+03 2.17e+01
  ... (remaining 7547 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    13.82: 10321
       13.82 -    27.64: 5
       27.64 -    41.46: 0
       41.46 -    55.29: 0
       55.29 -    69.11: 2
  Bond angle restraints: 10328
  Sorted by residual:
  angle pdb=" F3  ALF A1103 "
        pdb="AL   ALF A1103 "
        pdb=" F4  ALF A1103 "
      ideal   model   delta    sigma   weight residual
     109.63  178.74  -69.11 3.00e+00 1.11e-01 5.31e+02
  angle pdb=" F1  ALF A1103 "
        pdb="AL   ALF A1103 "
        pdb=" F2  ALF A1103 "
      ideal   model   delta    sigma   weight residual
     108.68  177.20  -68.52 3.00e+00 1.11e-01 5.22e+02
  angle pdb=" N   ILE A 783 "
        pdb=" CA  ILE A 783 "
        pdb=" CB  ILE A 783 "
      ideal   model   delta    sigma   weight residual
     111.41  123.55  -12.14 1.38e+00 5.25e-01 7.74e+01
  angle pdb=" F2  ALF A1103 "
        pdb="AL   ALF A1103 "
        pdb=" F3  ALF A1103 "
      ideal   model   delta    sigma   weight residual
     109.59   88.39   21.20 3.00e+00 1.11e-01 4.99e+01
  angle pdb=" F1  ALF A1103 "
        pdb="AL   ALF A1103 "
        pdb=" F4  ALF A1103 "
      ideal   model   delta    sigma   weight residual
     109.02   88.09   20.93 3.00e+00 1.11e-01 4.87e+01
  ... (remaining 10323 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.18: 4479
       33.18 -    66.37: 127
       66.37 -    99.55: 16
       99.55 -   132.73: 2
      132.73 -   165.91: 1
  Dihedral angle restraints: 4625
    sinusoidal: 2162
      harmonic: 2463
  Sorted by residual:
  dihedral pdb=" C5' ADP A1102 "
           pdb=" O5' ADP A1102 "
           pdb=" PA  ADP A1102 "
           pdb=" O2A ADP A1102 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  105.92 -165.91     1      2.00e+01 2.50e-03 4.73e+01
  dihedral pdb=" O2A ADP A1102 "
           pdb=" O3A ADP A1102 "
           pdb=" PA  ADP A1102 "
           pdb=" PB  ADP A1102 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   55.39 -115.39     1      2.00e+01 2.50e-03 3.43e+01
  dihedral pdb=" O1B ADP A1102 "
           pdb=" O3A ADP A1102 "
           pdb=" PB  ADP A1102 "
           pdb=" PA  ADP A1102 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   41.70 -101.71     1      2.00e+01 2.50e-03 2.89e+01
  ... (remaining 4622 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 900
       0.056 -    0.113: 240
       0.113 -    0.169: 32
       0.169 -    0.225: 2
       0.225 -    0.281: 3
  Chirality restraints: 1177
  Sorted by residual:
  chirality pdb=" CA  LYS A 782 "
            pdb=" N   LYS A 782 "
            pdb=" C   LYS A 782 "
            pdb=" CB  LYS A 782 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.28 2.00e-01 2.50e+01 1.98e+00
  chirality pdb=" CB  ILE A 479 "
            pdb=" CA  ILE A 479 "
            pdb=" CG1 ILE A 479 "
            pdb=" CG2 ILE A 479 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.26 2.00e-01 2.50e+01 1.75e+00
  chirality pdb=" CA  ILE A 783 "
            pdb=" N   ILE A 783 "
            pdb=" C   ILE A 783 "
            pdb=" CB  ILE A 783 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.17    0.26 2.00e-01 2.50e+01 1.74e+00
  ... (remaining 1174 not shown)

  Planarity restraints: 1210
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A 711 "    0.016 2.00e-02 2.50e+03   3.18e-02 1.01e+01
        pdb=" CD  GLN A 711 "   -0.055 2.00e-02 2.50e+03
        pdb=" OE1 GLN A 711 "    0.021 2.00e-02 2.50e+03
        pdb=" NE2 GLN A 711 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 377 "    0.021 2.00e-02 2.50e+03   1.79e-02 5.61e+00
        pdb=" CG  PHE A 377 "   -0.042 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 377 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 377 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 377 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 377 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 377 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 763 "   -0.003 2.00e-02 2.50e+03   1.67e-02 4.87e+00
        pdb=" CG  PHE A 763 "    0.032 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 763 "   -0.025 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 763 "   -0.012 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 763 "    0.008 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 763 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 763 "    0.006 2.00e-02 2.50e+03
  ... (remaining 1207 not shown)

  Histogram of nonbonded interaction distances:
        1.86 -     2.47: 39
        2.47 -     3.08: 5085
        3.08 -     3.68: 10739
        3.68 -     4.29: 15233
        4.29 -     4.90: 24550
  Nonbonded interactions: 55646
  Sorted by model distance:
  nonbonded pdb=" F4  ALF A1103 "
            pdb="MG    MG A1104 "
     model   vdw
     1.860 2.120
  nonbonded pdb=" O1B ADP A1102 "
            pdb=" F1  ALF A1103 "
     model   vdw
     2.119 2.990
  nonbonded pdb=" F1  ALF A1103 "
            pdb="MG    MG A1104 "
     model   vdw
     2.148 2.120
  nonbonded pdb=" NH2 ARG A 822 "
            pdb=" F3  ALF A1103 "
     model   vdw
     2.155 3.070
  nonbonded pdb=" O2B ADP A1102 "
            pdb=" F3  ALF A1103 "
     model   vdw
     2.166 2.990
  ... (remaining 55641 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.170
  Find NCS groups from input model:        0.030
  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:1.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
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      :  0.008   0.096   7556  Z= 0.375
  Angle     :  1.445  69.108  10334  Z= 0.631
  Chirality :  0.051   0.281   1177
  Planarity :  0.005   0.053   1210
  Dihedral  : 15.704 165.915   3023
  Min Nonbonded Distance : 1.860

Molprobity Statistics.
  All-atom Clashscore : 13.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.59 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.55 %
    Favored  : 99.32 %
  Cbeta Deviations :  0.12 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -1.52 (0.27), residues: 822
  helix: -0.02 (0.27), residues: 307
  sheet: -0.96 (0.37), residues: 164
  loop : -1.88 (0.30), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 824 
 TYR   0.019   0.003   TYR A 311 
 PHE   0.042   0.003   PHE A 377 
 TRP   0.011   0.002   TRP B 423 
 HIS   0.011   0.002   HIS A 835 

Details of bonding type rmsd
  covalent geometry    : bond        0.00806 ( 7552)
  covalent geometry    : angle       1.40343 (10328)
  hydrogen bonds       : bond        0.13591 (  334)
  hydrogen bonds       : angle       6.23491 (  936)
  metal coordination   : bond        0.01580 (    4)
  metal coordination   : angle      14.33987 (    6)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 182
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  333 SER cc_start: 0.8185 (p) cc_final: 0.7858 (t)
REVERT: A  391 SER cc_start: 0.8429 (p) cc_final: 0.8175 (p)
REVERT: A  529 LYS cc_start: 0.8656 (mmtp) cc_final: 0.8401 (tmtt)
REVERT: A  783 ILE cc_start: 0.9457 (mt) cc_final: 0.9171 (mm)
REVERT: A  853 MET cc_start: 0.8725 (ttm) cc_final: 0.8211 (ttm)
REVERT: A  875 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7199 (tp30)
REVERT: A  942 ARG cc_start: 0.8417 (ttp-110) cc_final: 0.7977 (ptt90)
REVERT: B  331 ARG cc_start: 0.4894 (mmt-90) cc_final: 0.4661 (mmt90)
REVERT: B  387 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7384 (mp0)
  outliers start: 1
  outliers final: 0
  residues processed: 183
  average time/residue: 0.1070
  time to fit residues: 24.6024
Evaluate side-chains
  96 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.0000
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.6984

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

Flipped N/Q/H residues before XYZ refinement:
A 505 HIS
A 562 GLN
A 784 ASN
A 877 GLN
B 343 HIS
B 436 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.101765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.080464 restraints weight = 34310.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.082706 restraints weight = 20766.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.083710 restraints weight = 13627.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.084235 restraints weight = 10540.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.084546 restraints weight = 9441.155|
|-----------------------------------------------------------------------------|
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3160
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3160 r_free = 0.3160    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3160 r_free = 0.3160    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3160
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.3164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7556  Z= 0.133
  Angle     :  0.957  30.796  10334  Z= 0.401
  Chirality :  0.042   0.152   1177
  Planarity :  0.004   0.051   1210
  Dihedral  : 14.146 152.660   1337
  Min Nonbonded Distance : 1.933

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  3.96 %
    Favored  : 95.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -0.43 (0.28), residues: 822
  helix:  1.07 (0.28), residues: 321
  sheet: -0.63 (0.37), residues: 173
  loop : -1.41 (0.33), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 674 
 TYR   0.016   0.002   TYR A 732 
 PHE   0.020   0.002   PHE B 335 
 TRP   0.018   0.002   TRP B 327 
 HIS   0.007   0.001   HIS B 436 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 7552)
  covalent geometry    : angle       0.91837 (10328)
  hydrogen bonds       : bond        0.04750 (  334)
  hydrogen bonds       : angle       4.57926 (  936)
  metal coordination   : bond        0.01392 (    4)
  metal coordination   : angle      11.14510 (    6)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 122
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  333 SER cc_start: 0.8077 (p) cc_final: 0.7681 (t)
REVERT: A  391 SER cc_start: 0.8528 (p) cc_final: 0.8252 (p)
REVERT: A  584 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7913 (pm20)
REVERT: A  686 MET cc_start: 0.7929 (tpp) cc_final: 0.7700 (tpp)
REVERT: A  853 MET cc_start: 0.8660 (ttm) cc_final: 0.8064 (ttm)
REVERT: A  854 MET cc_start: 0.8466 (tmm) cc_final: 0.8068 (tmm)
REVERT: A  875 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7150 (tp30)
REVERT: A  926 MET cc_start: 0.8252 (mtp) cc_final: 0.8043 (mtp)
REVERT: A  942 ARG cc_start: 0.8247 (ttp-110) cc_final: 0.7630 (tmm-80)
REVERT: B  348 ARG cc_start: 0.8213 (tpp80) cc_final: 0.7166 (ttm110)
REVERT: B  387 GLU cc_start: 0.7430 (mm-30) cc_final: 0.6801 (mm-30)
REVERT: B  465 TYR cc_start: 0.7230 (m-10) cc_final: 0.6865 (m-10)
  outliers start: 1
  outliers final: 0
  residues processed: 123
  average time/residue: 0.1034
  time to fit residues: 16.4240
Evaluate side-chains
  86 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 85
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 53 optimal weight:    4.9990
   chunk 22 optimal weight:    3.9990
   chunk 76 optimal weight:    1.9990
   chunk 58 optimal weight:    5.9990
   chunk 26 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 83 optimal weight:    4.9990
   chunk 55 optimal weight:    0.7980
   chunk 62 optimal weight:    8.9990
   chunk 7 optimal weight:    2.9990
   chunk 43 optimal weight:    0.0670
   overall best weight:    1.7724

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

Flipped N/Q/H residues before XYZ refinement:
A 524 ASN
** B 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 470 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.095401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.073785 restraints weight = 30625.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.075925 restraints weight = 18815.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.077146 restraints weight = 11261.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.077192 restraints weight = 9042.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.077258 restraints weight = 8662.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3030
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3030 r_free = 0.3030    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3030 r_free = 0.3030    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3030
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.4216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7556  Z= 0.192
  Angle     :  0.980  31.663  10334  Z= 0.418
  Chirality :  0.044   0.154   1177
  Planarity :  0.005   0.046   1210
  Dihedral  : 14.184 169.828   1337
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -0.31 (0.29), residues: 822
  helix:  1.17 (0.28), residues: 322
  sheet: -0.35 (0.40), residues: 158
  loop : -1.45 (0.32), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 348 
 TYR   0.017   0.002   TYR A 732 
 PHE   0.018   0.002   PHE B 335 
 TRP   0.018   0.002   TRP B 327 
 HIS   0.005   0.002   HIS A 752 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 ( 7552)
  covalent geometry    : angle       0.94867 (10328)
  hydrogen bonds       : bond        0.05655 (  334)
  hydrogen bonds       : angle       4.80075 (  936)
  metal coordination   : bond        0.00901 (    4)
  metal coordination   : angle      10.20703 (    6)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 SER cc_start: 0.8747 (m) cc_final: 0.8250 (p)
REVERT: A  600 CYS cc_start: 0.7822 (m) cc_final: 0.6461 (t)
REVERT: A  686 MET cc_start: 0.7916 (tpp) cc_final: 0.7619 (tpp)
REVERT: A  853 MET cc_start: 0.8723 (ttm) cc_final: 0.8031 (ttm)
REVERT: A  875 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7197 (tp30)
REVERT: A  879 GLN cc_start: 0.7401 (tt0) cc_final: 0.6427 (tp40)
REVERT: A  942 ARG cc_start: 0.8350 (ttp-110) cc_final: 0.7897 (tmm-80)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.0813
  time to fit residues: 12.0154
Evaluate side-chains
  83 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 10 optimal weight:    0.8980
   chunk 71 optimal weight:    4.9990
   chunk 23 optimal weight:    2.9990
   chunk 39 optimal weight:    4.9990
   chunk 18 optimal weight:    0.3980
   chunk 60 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   overall best weight:    1.5984

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

Flipped N/Q/H residues before XYZ refinement:
A 711 GLN
A 818 GLN
A 928 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.095013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.075046 restraints weight = 38817.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.077949 restraints weight = 24962.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.078218 restraints weight = 16030.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.078806 restraints weight = 11669.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.079130 restraints weight = 10267.761|
|-----------------------------------------------------------------------------|
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3062
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3062 r_free = 0.3062    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3062 r_free = 0.3062    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3062
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.4892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7556  Z= 0.175
  Angle     :  0.946  30.099  10334  Z= 0.398
  Chirality :  0.043   0.180   1177
  Planarity :  0.004   0.041   1210
  Dihedral  : 13.916 160.769   1337
  Min Nonbonded Distance : 1.946

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -0.05 (0.29), residues: 822
  helix:  1.19 (0.28), residues: 326
  sheet: -0.10 (0.40), residues: 167
  loop : -1.20 (0.34), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 348 
 TYR   0.019   0.002   TYR B 475 
 PHE   0.015   0.002   PHE B 335 
 TRP   0.017   0.002   TRP B 386 
 HIS   0.005   0.001   HIS B 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 7552)
  covalent geometry    : angle       0.92157 (10328)
  hydrogen bonds       : bond        0.05059 (  334)
  hydrogen bonds       : angle       4.76045 (  936)
  metal coordination   : bond        0.00797 (    4)
  metal coordination   : angle       8.94252 (    6)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 SER cc_start: 0.8818 (m) cc_final: 0.8328 (p)
REVERT: A  686 MET cc_start: 0.7976 (tpp) cc_final: 0.7616 (tpp)
REVERT: A  853 MET cc_start: 0.8663 (ttm) cc_final: 0.7962 (ttm)
REVERT: A  875 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7238 (tp30)
REVERT: A  879 GLN cc_start: 0.7474 (tt0) cc_final: 0.7072 (tp40)
REVERT: A  942 ARG cc_start: 0.8395 (ttp-110) cc_final: 0.8019 (tmm-80)
REVERT: B  389 ARG cc_start: 0.6860 (ttm170) cc_final: 0.6592 (ttm170)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.0833
  time to fit residues: 12.1779
Evaluate side-chains
  79 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 0 optimal weight:    5.9990
   chunk 50 optimal weight:    4.9990
   chunk 18 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 55 optimal weight:    3.9990
   chunk 4 optimal weight:    0.7980
   chunk 84 optimal weight:    6.9990
   chunk 70 optimal weight:    4.9990
   chunk 27 optimal weight:    6.9990
   overall best weight:    2.7386

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

Flipped N/Q/H residues before XYZ refinement:
A 371 GLN
A 531 GLN
B 478 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.091435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.072134 restraints weight = 41460.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.073435 restraints weight = 33615.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.074389 restraints weight = 21989.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.075283 restraints weight = 14474.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.075833 restraints weight = 12171.363|
|-----------------------------------------------------------------------------|
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2993
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2993 r_free = 0.2993    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2993 r_free = 0.2993    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2993
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.5442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058   7556  Z= 0.269
  Angle     :  1.027  29.706  10334  Z= 0.446
  Chirality :  0.047   0.182   1177
  Planarity :  0.005   0.048   1210
  Dihedral  : 14.305 177.608   1337
  Min Nonbonded Distance : 1.887

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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 (0.29), residues: 822
  helix:  0.90 (0.28), residues: 319
  sheet: -0.54 (0.42), residues: 152
  loop : -1.26 (0.31), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 689 
 TYR   0.019   0.002   TYR A 732 
 PHE   0.018   0.002   PHE B 335 
 TRP   0.019   0.002   TRP B 386 
 HIS   0.007   0.002   HIS A 835 

Details of bonding type rmsd
  covalent geometry    : bond        0.00606 ( 7552)
  covalent geometry    : angle       0.99614 (10328)
  hydrogen bonds       : bond        0.06324 (  334)
  hydrogen bonds       : angle       5.14032 (  936)
  metal coordination   : bond        0.01083 (    4)
  metal coordination   : angle      10.43178 (    6)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 SER cc_start: 0.8920 (m) cc_final: 0.8528 (p)
REVERT: A  686 MET cc_start: 0.7943 (tpp) cc_final: 0.7611 (tpp)
REVERT: A  853 MET cc_start: 0.8736 (ttm) cc_final: 0.8100 (ttm)
REVERT: A  875 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7675 (tp30)
REVERT: A  942 ARG cc_start: 0.8154 (ttp-110) cc_final: 0.7897 (tmm-80)
REVERT: B  345 TYR cc_start: 0.5944 (m-80) cc_final: 0.5711 (m-80)
REVERT: B  377 GLN cc_start: 0.4338 (mp10) cc_final: 0.3428 (mm-40)
REVERT: B  496 THR cc_start: 0.8988 (m) cc_final: 0.8531 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.0811
  time to fit residues: 11.2385
Evaluate side-chains
  80 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 20 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 76 optimal weight:    6.9990
   chunk 10 optimal weight:    0.5980
   chunk 28 optimal weight:    0.8980
   chunk 44 optimal weight:    2.9990
   chunk 68 optimal weight:    0.0870
   chunk 32 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   overall best weight:    0.9160

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

Flipped N/Q/H residues before XYZ refinement:
A 771 GLN
** B 383 HIS ** 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 = 0.3372 r_free = 0.3372 target = 0.096686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.076274 restraints weight = 44862.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.079308 restraints weight = 36769.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.079875 restraints weight = 20742.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.080723 restraints weight = 14292.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.081125 restraints weight = 11876.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3088
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3088 r_free = 0.3088    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3088 r_free = 0.3088    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3088
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.5720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7556  Z= 0.130
  Angle     :  0.925  30.353  10334  Z= 0.381
  Chirality :  0.042   0.159   1177
  Planarity :  0.004   0.043   1210
  Dihedral  : 13.771 150.538   1337
  Min Nonbonded Distance : 1.910

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.13 (0.30), residues: 822
  helix:  1.36 (0.29), residues: 330
  sheet: -0.26 (0.40), residues: 171
  loop : -1.02 (0.34), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 348 
 TYR   0.013   0.001   TYR A 732 
 PHE   0.018   0.001   PHE A 763 
 TRP   0.029   0.002   TRP B 386 
 HIS   0.004   0.001   HIS A 603 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 7552)
  covalent geometry    : angle       0.89503 (10328)
  hydrogen bonds       : bond        0.04599 (  334)
  hydrogen bonds       : angle       4.60605 (  936)
  metal coordination   : bond        0.00725 (    4)
  metal coordination   : angle       9.68138 (    6)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 SER cc_start: 0.8834 (m) cc_final: 0.8448 (p)
REVERT: A  793 GLU cc_start: 0.8236 (pt0) cc_final: 0.7914 (pt0)
REVERT: A  853 MET cc_start: 0.8712 (ttm) cc_final: 0.8056 (ttm)
REVERT: A  875 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7667 (tp30)
REVERT: B  330 TYR cc_start: 0.7617 (t80) cc_final: 0.7383 (t80)
REVERT: B  377 GLN cc_start: 0.4314 (mp10) cc_final: 0.3238 (mm-40)
REVERT: B  379 PHE cc_start: 0.6904 (m-80) cc_final: 0.6610 (m-80)
REVERT: B  453 MET cc_start: 0.5302 (mmp) cc_final: 0.4775 (mmp)
REVERT: B  470 GLN cc_start: 0.8268 (mm110) cc_final: 0.7576 (pp30)
REVERT: B  496 THR cc_start: 0.8978 (m) cc_final: 0.8616 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.0819
  time to fit residues: 12.8584
Evaluate side-chains
  81 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:   10.0000
   chunk 31 optimal weight:    3.9990
   chunk 26 optimal weight:    0.7980
   chunk 0 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   chunk 81 optimal weight:   10.0000
   chunk 36 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   chunk 85 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
** B 383 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 = 0.3344 r_free = 0.3344 target = 0.094621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.074604 restraints weight = 23086.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.075557 restraints weight = 14670.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.076160 restraints weight = 11544.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.076144 restraints weight = 9850.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.077197 restraints weight = 9533.153|
|-----------------------------------------------------------------------------|
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3022
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3022 r_free = 0.3022    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3022 r_free = 0.3022    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3022
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.5874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7556  Z= 0.168
  Angle     :  0.957  30.155  10334  Z= 0.400
  Chirality :  0.043   0.147   1177
  Planarity :  0.004   0.042   1210
  Dihedral  : 13.899 161.296   1337
  Min Nonbonded Distance : 1.946

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -0.01 (0.29), residues: 822
  helix:  1.30 (0.29), residues: 331
  sheet: -0.30 (0.41), residues: 161
  loop : -1.18 (0.33), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 348 
 TYR   0.012   0.002   TYR A 732 
 PHE   0.013   0.001   PHE B 464 
 TRP   0.028   0.002   TRP B 386 
 HIS   0.005   0.001   HIS B 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 7552)
  covalent geometry    : angle       0.92569 (10328)
  hydrogen bonds       : bond        0.05033 (  334)
  hydrogen bonds       : angle       4.71606 (  936)
  metal coordination   : bond        0.00964 (    4)
  metal coordination   : angle      10.09530 (    6)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 SER cc_start: 0.8736 (m) cc_final: 0.8332 (p)
REVERT: A  686 MET cc_start: 0.7609 (tpp) cc_final: 0.7316 (tmm)
REVERT: A  793 GLU cc_start: 0.8105 (pt0) cc_final: 0.7781 (pt0)
REVERT: A  853 MET cc_start: 0.8815 (ttm) cc_final: 0.8260 (ttm)
REVERT: A  854 MET cc_start: 0.8652 (tmm) cc_final: 0.8162 (tmm)
REVERT: A  875 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7682 (tp30)
REVERT: B  331 ARG cc_start: 0.7188 (mpt180) cc_final: 0.4947 (mmt-90)
REVERT: B  377 GLN cc_start: 0.4616 (mp10) cc_final: 0.3581 (mm-40)
REVERT: B  379 PHE cc_start: 0.7028 (m-80) cc_final: 0.6595 (m-10)
REVERT: B  453 MET cc_start: 0.5138 (mmp) cc_final: 0.4154 (mmp)
REVERT: B  470 GLN cc_start: 0.8092 (mm110) cc_final: 0.7432 (pp30)
REVERT: B  496 THR cc_start: 0.8924 (m) cc_final: 0.8530 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 98
  average time/residue: 0.0781
  time to fit residues: 10.6779
Evaluate side-chains
  78 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 82 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0170
   chunk 32 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 77 optimal weight:    6.9990
   chunk 72 optimal weight:    3.9990
   overall best weight:    1.2024

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

Flipped N/Q/H residues before XYZ refinement:
** B 383 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 = 0.3350 r_free = 0.3350 target = 0.095276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.075494 restraints weight = 43350.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.076600 restraints weight = 36806.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.078091 restraints weight = 24014.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.078690 restraints weight = 15461.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.079334 restraints weight = 13189.220|
|-----------------------------------------------------------------------------|
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3056
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3056 r_free = 0.3056    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3056 r_free = 0.3056    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3056
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.6023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7556  Z= 0.146
  Angle     :  0.930  30.245  10334  Z= 0.386
  Chirality :  0.042   0.164   1177
  Planarity :  0.004   0.064   1210
  Dihedral  : 13.814 156.669   1337
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.06 (0.29), residues: 822
  helix:  1.35 (0.29), residues: 333
  sheet: -0.22 (0.41), residues: 161
  loop : -1.16 (0.33), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 348 
 TYR   0.014   0.001   TYR A 732 
 PHE   0.012   0.001   PHE B 477 
 TRP   0.027   0.002   TRP B 386 
 HIS   0.004   0.001   HIS A 603 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 7552)
  covalent geometry    : angle       0.90342 (10328)
  hydrogen bonds       : bond        0.04702 (  334)
  hydrogen bonds       : angle       4.69365 (  936)
  metal coordination   : bond        0.00835 (    4)
  metal coordination   : angle       9.29210 (    6)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 SER cc_start: 0.8825 (m) cc_final: 0.8422 (p)
REVERT: A  793 GLU cc_start: 0.8208 (pt0) cc_final: 0.7823 (pt0)
REVERT: A  853 MET cc_start: 0.8768 (ttm) cc_final: 0.8227 (ttm)
REVERT: A  875 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7636 (tp30)
REVERT: B  331 ARG cc_start: 0.7094 (mpt180) cc_final: 0.5012 (mmt-90)
REVERT: B  350 ASP cc_start: 0.7861 (m-30) cc_final: 0.7498 (m-30)
REVERT: B  379 PHE cc_start: 0.6894 (m-80) cc_final: 0.6570 (m-80)
REVERT: B  453 MET cc_start: 0.5125 (mmp) cc_final: 0.4636 (mmp)
REVERT: B  496 THR cc_start: 0.8938 (m) cc_final: 0.8530 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 97
  average time/residue: 0.0786
  time to fit residues: 10.5664
Evaluate side-chains
  79 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 80 optimal weight:    0.9990
   chunk 23 optimal weight:    0.7980
   chunk 64 optimal weight:    2.9990
   chunk 77 optimal weight:   10.0000
   chunk 1 optimal weight:    5.9990
   chunk 13 optimal weight:    0.1980
   chunk 6 optimal weight:    0.9990
   chunk 48 optimal weight:    0.8980
   chunk 29 optimal weight:    0.6980
   chunk 60 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   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 455 ASN
B 332 ASN
** B 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.097366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.077460 restraints weight = 56784.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.080547 restraints weight = 44842.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.082264 restraints weight = 20581.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.082834 restraints weight = 13903.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.083476 restraints weight = 11249.190|
|-----------------------------------------------------------------------------|
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3114
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3114 r_free = 0.3114    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3114 r_free = 0.3114    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3114
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.6181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   7556  Z= 0.116
  Angle     :  0.903  30.106  10334  Z= 0.369
  Chirality :  0.041   0.176   1177
  Planarity :  0.004   0.046   1210
  Dihedral  : 13.641 145.414   1337
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.00 %
    Favored  : 99.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.38 (0.30), residues: 822
  helix:  1.59 (0.29), residues: 333
  sheet:  0.06 (0.41), residues: 173
  loop : -1.06 (0.34), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 348 
 TYR   0.014   0.001   TYR A 732 
 PHE   0.010   0.001   PHE B 477 
 TRP   0.023   0.002   TRP B 386 
 HIS   0.005   0.001   HIS B 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 7552)
  covalent geometry    : angle       0.88115 (10328)
  hydrogen bonds       : bond        0.04156 (  334)
  hydrogen bonds       : angle       4.39646 (  936)
  metal coordination   : bond        0.00696 (    4)
  metal coordination   : angle       8.17062 (    6)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 106
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 SER cc_start: 0.8768 (m) cc_final: 0.8415 (p)
REVERT: A  391 SER cc_start: 0.8781 (p) cc_final: 0.8423 (t)
REVERT: A  455 ASN cc_start: 0.7745 (OUTLIER) cc_final: 0.6783 (t0)
REVERT: A  793 GLU cc_start: 0.8228 (pt0) cc_final: 0.7757 (pt0)
REVERT: A  853 MET cc_start: 0.8807 (ttm) cc_final: 0.8271 (ttm)
REVERT: A  854 MET cc_start: 0.8649 (tmm) cc_final: 0.8259 (tmm)
REVERT: A  875 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7623 (tp30)
REVERT: A  926 MET cc_start: 0.8657 (mtp) cc_final: 0.8282 (mtt)
REVERT: B  331 ARG cc_start: 0.7171 (mpt180) cc_final: 0.5185 (mmt-90)
REVERT: B  349 GLN cc_start: 0.7565 (mp10) cc_final: 0.7030 (tm-30)
REVERT: B  350 ASP cc_start: 0.7776 (m-30) cc_final: 0.7470 (m-30)
REVERT: B  379 PHE cc_start: 0.7051 (m-80) cc_final: 0.6676 (m-80)
REVERT: B  453 MET cc_start: 0.5063 (mmp) cc_final: 0.4031 (mmp)
REVERT: B  475 TYR cc_start: 0.7769 (t80) cc_final: 0.7529 (t80)
REVERT: B  496 THR cc_start: 0.8958 (m) cc_final: 0.8551 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 107
  average time/residue: 0.0733
  time to fit residues: 10.8255
Evaluate side-chains
  82 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 81
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9990
   chunk 36 optimal weight:    4.9990
   chunk 72 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   chunk 2 optimal weight:    0.0980
   chunk 75 optimal weight:   10.0000
   chunk 37 optimal weight:    6.9990
   chunk 8 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   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 455 ASN
** B 383 HIS ** 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 = 0.3389 r_free = 0.3389 target = 0.097435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.078806 restraints weight = 41252.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.080433 restraints weight = 35484.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.081399 restraints weight = 21262.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.082125 restraints weight = 13667.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.082626 restraints weight = 11666.869|
|-----------------------------------------------------------------------------|
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3109
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3109 r_free = 0.3109    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3109 r_free = 0.3109    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3109
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.6321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7556  Z= 0.116
  Angle     :  0.901  30.034  10334  Z= 0.368
  Chirality :  0.041   0.171   1177
  Planarity :  0.004   0.045   1210
  Dihedral  : 13.620 144.379   1337
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.54 (0.30), residues: 822
  helix:  1.69 (0.29), residues: 333
  sheet:  0.29 (0.42), residues: 167
  loop : -1.01 (0.34), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 348 
 TYR   0.012   0.001   TYR A 732 
 PHE   0.028   0.001   PHE B 477 
 TRP   0.019   0.001   TRP B 386 
 HIS   0.004   0.001   HIS A 603 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 7552)
  covalent geometry    : angle       0.88149 (10328)
  hydrogen bonds       : bond        0.04102 (  334)
  hydrogen bonds       : angle       4.39187 (  936)
  metal coordination   : bond        0.00606 (    4)
  metal coordination   : angle       7.72340 (    6)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 SER cc_start: 0.8776 (m) cc_final: 0.8406 (p)
REVERT: A  490 SER cc_start: 0.9188 (p) cc_final: 0.8550 (m)
REVERT: A  793 GLU cc_start: 0.8256 (pt0) cc_final: 0.7803 (pt0)
REVERT: A  853 MET cc_start: 0.8768 (ttm) cc_final: 0.8171 (ttm)
REVERT: A  854 MET cc_start: 0.8690 (tmm) cc_final: 0.8330 (tmm)
REVERT: A  865 LYS cc_start: 0.8906 (tppt) cc_final: 0.8488 (tppt)
REVERT: A  875 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7589 (tp30)
REVERT: B  331 ARG cc_start: 0.7153 (mpt180) cc_final: 0.5167 (mmt-90)
REVERT: B  349 GLN cc_start: 0.7461 (mp10) cc_final: 0.6970 (tm-30)
REVERT: B  350 ASP cc_start: 0.7826 (m-30) cc_final: 0.7323 (m-30)
REVERT: B  379 PHE cc_start: 0.7089 (m-80) cc_final: 0.6751 (m-80)
REVERT: B  453 MET cc_start: 0.4756 (mmp) cc_final: 0.3474 (mmp)
REVERT: B  496 THR cc_start: 0.8975 (m) cc_final: 0.8512 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.0778
  time to fit residues: 11.1646
Evaluate side-chains
  83 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 80 optimal weight:    0.0670
   chunk 58 optimal weight:    4.9990
   chunk 85 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 81 optimal weight:   10.0000
   chunk 79 optimal weight:    5.9990
   chunk 84 optimal weight:    5.9990
   chunk 38 optimal weight:    0.8980
   chunk 68 optimal weight:    5.9990
   chunk 43 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   overall best weight:    1.1522

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

Flipped N/Q/H residues before XYZ refinement:
A 455 ASN
** B 383 HIS ** 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 = 0.3368 r_free = 0.3368 target = 0.096139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.077411 restraints weight = 34269.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.078542 restraints weight = 29452.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.079358 restraints weight = 21605.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.080261 restraints weight = 14433.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.080581 restraints weight = 12088.732|
|-----------------------------------------------------------------------------|
r_work (final): 0.3084
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3084
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3084 r_free = 0.3084    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3084 r_free = 0.3084    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3084
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.6313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7556  Z= 0.141
  Angle     :  0.919  30.073  10334  Z= 0.381
  Chirality :  0.042   0.167   1177
  Planarity :  0.004   0.044   1210
  Dihedral  : 13.689 148.461   1337
  Min Nonbonded Distance : 1.982

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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 (0.30), residues: 822
  helix:  1.61 (0.29), residues: 333
  sheet:  0.19 (0.41), residues: 168
  loop : -1.00 (0.34), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 348 
 TYR   0.013   0.001   TYR A 732 
 PHE   0.010   0.001   PHE A 550 
 TRP   0.022   0.002   TRP B 386 
 HIS   0.007   0.001   HIS B 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 7552)
  covalent geometry    : angle       0.89827 (10328)
  hydrogen bonds       : bond        0.04456 (  334)
  hydrogen bonds       : angle       4.56581 (  936)
  metal coordination   : bond        0.00728 (    4)
  metal coordination   : angle       8.17467 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1150.25 seconds
wall clock time: 20 minutes 34.75 seconds (1234.75 seconds total)