Starting phenix.real_space_refine
on Thu Sep 18 14:04:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9byp_45041/09_2025/9byp_45041.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9byp_45041/09_2025/9byp_45041.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9byp_45041/09_2025/9byp_45041.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9byp_45041/09_2025/9byp_45041.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9byp_45041/09_2025/9byp_45041.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9byp_45041/09_2025/9byp_45041.cif"
  }
  resolution = 2.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.016
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P      11      5.49       5
     S      47      5.16       5
     C    5258      2.51       5
     N    1438      2.21       5
     O    1873      1.98       5
     H    8681      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 55 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 17309
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 14617
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 948, 14593
          Classifications: {'peptide': 948}
          Link IDs: {'PTRANS': 63, 'TRANS': 884}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 948, 14593
          Classifications: {'peptide': 948}
          Link IDs: {'PTRANS': 63, 'TRANS': 884}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 14750
    Chain: "C"
      Number of atoms: 376
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 376
          Classifications: {'DNA': 12}
          Modifications used: {'3*END': 1, '5*END': 1}
          Link IDs: {'rna3p': 11}
    Chain: "B"
      Number of atoms: 1472
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 1472
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 1, 'TRANS': 97}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 817
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 273, 817
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1, 'water': 272}
          Link IDs: {None: 272}
    Chain: "C"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 6
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 21
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 21
          Classifications: {'water': 7}
          Link IDs: {None: 6}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   6687  SG  CYS A 453      41.438  65.878  81.381  1.00 57.64           S
  ATOM   6727  SG  CYS A 456      44.522  67.319  80.372  1.00 53.48           S
  ATOM   6833  SG  CYS A 464      43.501  64.530  78.586  1.00 59.44           S

  Time building chain proxies: 4.23, per 1000 atoms: 0.24
  Number of scatterers: 17309
  At special positions: 0
  Unit cell: (89.04, 91.56, 112.56, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      1     29.99
     S      47     16.00
     P      11     15.00
     O    1873      8.00
     N    1438      7.00
     C    5258      6.00
     H    8681      1.00
    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: 1.57
  Conformation dependent library (CDL) restraints added in 791.5 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A2000 "
        pdb="ZN    ZN A2000 " - pdb=" SG  CYS A 456 "
        pdb="ZN    ZN A2000 " - pdb=" SG  CYS A 464 "
        pdb="ZN    ZN A2000 " - pdb=" SG  CYS A 453 "


  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1948

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 7 sheets defined
      51.3% alpha, 19.4% beta
      0 base pairs and 5 stacking pairs defined.
    Time for finding SS restraints: 2.55
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 15
    Processing helix  chain 'A' and resid 32 through 40
      removed outlier: 3.560A  pdb=" N   THR A  38 " --> pdb=" O   ARG A  34 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   LEU A  39 " --> pdb=" O   GLU A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 99
    Processing helix  chain 'A' and resid 107 through 119
      removed outlier: 3.727A  pdb=" N   GLU A 117 " --> pdb=" O   GLY A 113 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   VAL A 118 " --> pdb=" O   GLU A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 137
    Processing helix  chain 'A' and resid 143 through 145
      No H-bonds generated for 'chain 'A' and resid 143 through 145'
    Processing helix  chain 'A' and resid 157 through 163
    Processing helix  chain 'A' and resid 170 through 173
    Processing helix  chain 'A' and resid 192 through 194
      No H-bonds generated for 'chain 'A' and resid 192 through 194'
    Processing helix  chain 'A' and resid 199 through 203
    Processing helix  chain 'A' and resid 206 through 217
    Processing helix  chain 'A' and resid 217 through 225
      removed outlier: 3.732A  pdb=" N   LEU A 221 " --> pdb=" O   LEU A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 243
    Processing helix  chain 'A' and resid 251 through 255
    Processing helix  chain 'A' and resid 258 through 263
    Processing helix  chain 'A' and resid 266 through 291
      Proline residue:  A 286  - end of helix
    Processing helix  chain 'A' and resid 296 through 308
      removed outlier: 4.791A  pdb=" N   TYR A 301 " --> pdb=" O   SER A 298 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   ASP A 302 " --> pdb=" O   LEU A 299 " (cutoff:3.500A)
      Proline residue:  A 305  - end of helix
    Processing helix  chain 'A' and resid 311 through 337
      removed outlier: 4.399A  pdb=" N   ALA A 315 " --> pdb=" O   GLU A 311 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   LEU A 327 " --> pdb=" O   TYR A 323 " (cutoff:3.500A)
      Proline residue:  A 329  - end of helix
    Processing helix  chain 'A' and resid 340 through 342
      No H-bonds generated for 'chain 'A' and resid 340 through 342'
    Processing helix  chain 'A' and resid 357 through 360
    Processing helix  chain 'A' and resid 367 through 373
      removed outlier: 3.669A  pdb=" N   GLU A 373 " --> pdb=" O   GLY A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 410
      removed outlier: 3.624A  pdb=" N   LEU A 406 " --> pdb=" O   ALA A 402 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 425
    Processing helix  chain 'A' and resid 439 through 445
    Processing helix  chain 'A' and resid 446 through 450
    Processing helix  chain 'A' and resid 464 through 473
    Processing helix  chain 'A' and resid 474 through 476
      No H-bonds generated for 'chain 'A' and resid 474 through 476'
    Processing helix  chain 'A' and resid 526 through 540
    Processing helix  chain 'A' and resid 555 through 584
      removed outlier: 3.549A  pdb=" N   PHE A 563 " --> pdb=" O   PHE A 559 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 594
      removed outlier: 3.539A  pdb=" N   LEU A 591 " --> pdb=" O   THR A 587 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   LYS A 593 " --> pdb=" O   LYS A 589 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   SER A 594 " --> pdb=" O   ASP A 590 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 604 through 608
      removed outlier: 3.741A  pdb=" N   GLN A 608 " --> pdb=" O   PRO A 605 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 611 through 641
      removed outlier: 3.728A  pdb=" N   THR A 615 " --> pdb=" O   CYS A 611 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   GLN A 616 " --> pdb=" O   PRO A 612 " (cutoff:3.500A)
      Proline residue:  A 632  - end of helix
    Processing helix  chain 'A' and resid 647 through 667
      removed outlier: 4.093A  pdb=" N   GLY A 654 " --> pdb=" O   GLU A 650 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   GLN A 657 " --> pdb=" O   LYS A 653 " (cutoff:3.500A)
      removed outlier: 5.839A  pdb=" N   THR A 658 " --> pdb=" O   GLY A 654 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   THR A 661 " --> pdb=" O   GLN A 657 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 691 through 697
      removed outlier: 3.874A  pdb=" N   GLN A 697 " --> pdb=" O   ASP A 693 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 735 through 739
    Processing helix  chain 'A' and resid 746 through 750
      removed outlier: 3.862A  pdb=" N   TYR A 749 " --> pdb=" O   ARG A 746 " (cutoff:3.500A)
      removed outlier: 4.594A  pdb=" N   ILE A 750 " --> pdb=" O   GLU A 747 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 746 through 750'
    Processing helix  chain 'A' and resid 755 through 762
    Processing helix  chain 'A' and resid 762 through 767
    Processing helix  chain 'A' and resid 773 through 785
    Processing helix  chain 'A' and resid 794 through 816
    Processing helix  chain 'A' and resid 824 through 841
    Processing helix  chain 'A' and resid 864 through 871
      Proline residue:  A 867  - end of helix
    Processing helix  chain 'A' and resid 877 through 886
    Processing helix  chain 'A' and resid 900 through 907
      removed outlier: 3.933A  pdb=" N   VAL A 904 " --> pdb=" O   CYS A 900 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ALA A 907 " --> pdb=" O   GLN A 903 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 944 through 948
    Processing helix  chain 'B' and resid 989 through 1004
      removed outlier: 3.500A  pdb=" N   ASN B 993 " --> pdb=" O   TYR B 989 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1010 through 1023
    Processing helix  chain 'B' and resid 1024 through 1029
    Processing helix  chain 'B' and resid 1030 through 1038
    Processing helix  chain 'B' and resid 1039 through 1043
      removed outlier: 3.590A  pdb=" N   SER B1042 " --> pdb=" O   GLY B1039 " (cutoff:3.500A)
      removed outlier: 5.655A  pdb=" N   VAL B1043 " --> pdb=" O   ARG B1040 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 1039 through 1043'
    Processing helix  chain 'B' and resid 1044 through 1057
    Processing helix  chain 'B' and resid 1063 through 1075
      removed outlier: 3.954A  pdb=" N   TRP B1075 " --> pdb=" O   LEU B1071 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 18
      removed outlier: 7.113A  pdb=" N   GLY A  18 " --> pdb=" O   LEU A  70 " (cutoff:3.500A)
      removed outlier: 8.747A  pdb=" N   ARG A  72 " --> pdb=" O   GLY A  18 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   LEU A  80 " --> pdb=" O   HIS A  71 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 52
      removed outlier: 6.891A  pdb=" N   ASP A  89 " --> pdb=" O   ILE A 153 " (cutoff:3.500A)
      removed outlier: 5.332A  pdb=" N   ILE A 153 " --> pdb=" O   ASP A  89 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   GLY A 149 " --> pdb=" O   PHE A  93 " (cutoff:3.500A)
      removed outlier: 7.098A  pdb=" N   ALA A 182 " --> pdb=" O   PRO A  27 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 52
      removed outlier: 6.891A  pdb=" N   ASP A  89 " --> pdb=" O   ILE A 153 " (cutoff:3.500A)
      removed outlier: 5.332A  pdb=" N   ILE A 153 " --> pdb=" O   ASP A  89 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   GLY A 149 " --> pdb=" O   PHE A  93 " (cutoff:3.500A)
      removed outlier: 7.098A  pdb=" N   ALA A 182 " --> pdb=" O   PRO A  27 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 344 through 349
      removed outlier: 3.683A  pdb=" N   GLY A 346 " --> pdb=" O   THR A 365 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 488 through 493
      removed outlier: 22.849A  pdb=" N   ILE A 929 " --> pdb=" O   PRO A 717 " (cutoff:3.500A)
      removed outlier: 17.190A  pdb=" N   ASN A 719 " --> pdb=" O   ILE A 929 " (cutoff:3.500A)
      removed outlier: 12.361A  pdb=" N   GLN A 931 " --> pdb=" O   ASN A 719 " (cutoff:3.500A)
      removed outlier: 8.472A  pdb=" N   LYS A 721 " --> pdb=" O   GLN A 931 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   GLY A 933 " --> pdb=" O   LYS A 721 " (cutoff:3.500A)
      removed outlier: 7.417A  pdb=" N   ARG A 725 " --> pdb=" O   LEU A 935 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   THR A 674 " --> pdb=" O   ARG A 718 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 596 through 602
      removed outlier: 22.849A  pdb=" N   ILE A 929 " --> pdb=" O   PRO A 717 " (cutoff:3.500A)
      removed outlier: 17.190A  pdb=" N   ASN A 719 " --> pdb=" O   ILE A 929 " (cutoff:3.500A)
      removed outlier: 12.361A  pdb=" N   GLN A 931 " --> pdb=" O   ASN A 719 " (cutoff:3.500A)
      removed outlier: 8.472A  pdb=" N   LYS A 721 " --> pdb=" O   GLN A 931 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   GLY A 933 " --> pdb=" O   LYS A 721 " (cutoff:3.500A)
      removed outlier: 7.417A  pdb=" N   ARG A 725 " --> pdb=" O   LEU A 935 " (cutoff:3.500A)
      removed outlier: 8.395A  pdb=" N   PHE A 968 " --> pdb=" O   PRO A 914 " (cutoff:3.500A)
      removed outlier: 14.096A  pdb=" N   THR A 916 " --> pdb=" O   LYS A 966 " (cutoff:3.500A)
      removed outlier: 16.743A  pdb=" N   LYS A 966 " --> pdb=" O   THR A 916 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   GLY A 853 " --> pdb=" O   THR A 898 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 786 through 788

    416 hydrogen bonds defined for protein.
    1140 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      5 stacking parallelities
  Total time for adding SS restraints: 3.40

  Time building geometry restraints manager: 2.18 seconds

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

  Histogram of bond lengths:
        0.90 -     1.09: 2911
        1.09 -     1.27: 7093
        1.27 -     1.46: 2525
        1.46 -     1.64: 4652
        1.64 -     1.83: 65
  Bond restraints: 17246
  Sorted by residual:
  bond pdb=" N   CYS A 900 "
       pdb=" H   CYS A 900 "
    ideal  model  delta    sigma   weight residual
    0.860  1.012 -0.152 2.00e-02 2.50e+03 5.76e+01
  bond pdb=" N   ARG B1068 "
       pdb=" H   ARG B1068 "
    ideal  model  delta    sigma   weight residual
    0.860  1.012 -0.152 2.00e-02 2.50e+03 5.75e+01
  bond pdb=" NH2 ARG A 857 "
       pdb="HH22 ARG A 857 "
    ideal  model  delta    sigma   weight residual
    0.860  1.012 -0.152 2.00e-02 2.50e+03 5.74e+01
  bond pdb=" N   GLY A 389 "
       pdb=" H   GLY A 389 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.74e+01
  bond pdb=" N   LEU A 705 "
       pdb=" H   LEU A 705 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.73e+01
  ... (remaining 17241 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.68: 25399
        2.68 -     5.36: 3970
        5.36 -     8.03: 971
        8.03 -    10.71: 21
       10.71 -    13.39: 24
  Bond angle restraints: 30385
  Sorted by residual:
  angle pdb=" CA  ASP A 274 "
        pdb=" CB  ASP A 274 "
        pdb=" CG  ASP A 274 "
      ideal   model   delta    sigma   weight residual
     112.60  119.21   -6.61 1.00e+00 1.00e+00 4.37e+01
  angle pdb=" CA  ASP A 377 "
        pdb=" CB  ASP A 377 "
        pdb=" CG  ASP A 377 "
      ideal   model   delta    sigma   weight residual
     112.60  119.08   -6.48 1.00e+00 1.00e+00 4.20e+01
  angle pdb=" CA  ASP A 544 "
        pdb=" CB  ASP A 544 "
        pdb=" CG  ASP A 544 "
      ideal   model   delta    sigma   weight residual
     112.60  118.85   -6.25 1.00e+00 1.00e+00 3.91e+01
  angle pdb=" C   THR A 872 "
        pdb=" N   ARG A 873 "
        pdb=" CA  ARG A 873 "
      ideal   model   delta    sigma   weight residual
     120.82  129.49   -8.67 1.47e+00 4.63e-01 3.48e+01
  angle pdb=" CA  ASN A 533 "
        pdb=" CB  ASN A 533 "
        pdb=" CG  ASN A 533 "
      ideal   model   delta    sigma   weight residual
     112.60  118.44   -5.84 1.00e+00 1.00e+00 3.41e+01
  ... (remaining 30380 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.61: 7197
       17.61 -    35.22: 422
       35.22 -    52.83: 173
       52.83 -    70.44: 122
       70.44 -    88.05: 7
  Dihedral angle restraints: 7921
    sinusoidal: 4344
      harmonic: 3577
  Sorted by residual:
  dihedral pdb=" CA  SER B1058 "
           pdb=" C   SER B1058 "
           pdb=" N   GLY B1059 "
           pdb=" CA  GLY B1059 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.81   28.19     0      5.00e+00 4.00e-02 3.18e+01
  dihedral pdb=" CA  SER A 962 "
           pdb=" C   SER A 962 "
           pdb=" N   SER A 963 "
           pdb=" CA  SER A 963 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.36   26.64     0      5.00e+00 4.00e-02 2.84e+01
  dihedral pdb=" CA  PRO A 909 "
           pdb=" C   PRO A 909 "
           pdb=" N   VAL A 910 "
           pdb=" CA  VAL A 910 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.83   23.17     0      5.00e+00 4.00e-02 2.15e+01
  ... (remaining 7918 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.075: 689
       0.075 -    0.149: 415
       0.149 -    0.224: 152
       0.224 -    0.298: 37
       0.298 -    0.373: 7
  Chirality restraints: 1300
  Sorted by residual:
  chirality pdb=" CA  PRO A 648 "
            pdb=" N   PRO A 648 "
            pdb=" C   PRO A 648 "
            pdb=" CB  PRO A 648 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.35    0.37 2.00e-01 2.50e+01 3.47e+00
  chirality pdb=" CA  ARG A 965 "
            pdb=" N   ARG A 965 "
            pdb=" C   ARG A 965 "
            pdb=" CB  ARG A 965 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.42e+00
  chirality pdb=" CA  ASP A 302 "
            pdb=" N   ASP A 302 "
            pdb=" C   ASP A 302 "
            pdb=" CB  ASP A 302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.20e+00
  ... (remaining 1297 not shown)

  Planarity restraints: 2476
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 228 "   -0.483 9.50e-02 1.11e+02   1.91e-01 2.64e+02
        pdb=" NE  ARG A 228 "   -0.020 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 228 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 228 "   -0.031 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 228 "    0.014 2.00e-02 2.50e+03
        pdb="HH11 ARG A 228 "    0.172 2.00e-02 2.50e+03
        pdb="HH12 ARG A 228 "   -0.199 2.00e-02 2.50e+03
        pdb="HH21 ARG A 228 "   -0.056 2.00e-02 2.50e+03
        pdb="HH22 ARG A 228 "    0.147 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B1031 "    0.387 9.50e-02 1.11e+02   1.61e-01 2.26e+02
        pdb=" NE  ARG B1031 "    0.075 2.00e-02 2.50e+03
        pdb=" CZ  ARG B1031 "    0.052 2.00e-02 2.50e+03
        pdb=" NH1 ARG B1031 "    0.098 2.00e-02 2.50e+03
        pdb=" NH2 ARG B1031 "   -0.010 2.00e-02 2.50e+03
        pdb="HH11 ARG B1031 "   -0.222 2.00e-02 2.50e+03
        pdb="HH12 ARG B1031 "    0.094 2.00e-02 2.50e+03
        pdb="HH21 ARG B1031 "   -0.085 2.00e-02 2.50e+03
        pdb="HH22 ARG B1031 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 810 "    0.072 9.50e-02 1.11e+02   8.96e-02 1.68e+02
        pdb=" NE  ARG A 810 "    0.025 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 810 "    0.015 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 810 "   -0.014 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 810 "   -0.001 2.00e-02 2.50e+03
        pdb="HH11 ARG A 810 "   -0.118 2.00e-02 2.50e+03
        pdb="HH12 ARG A 810 "    0.173 2.00e-02 2.50e+03
        pdb="HH21 ARG A 810 "    0.055 2.00e-02 2.50e+03
        pdb="HH22 ARG A 810 "   -0.138 2.00e-02 2.50e+03
  ... (remaining 2473 not shown)

  Histogram of nonbonded interaction distances:
        1.57 -     2.18: 1339
        2.18 -     2.78: 28469
        2.78 -     3.39: 49601
        3.39 -     3.99: 69764
        3.99 -     4.60: 98426
  Nonbonded interactions: 247599
  Sorted by model distance:
  nonbonded pdb="HD21AASN A 300 "
            pdb=" OG  SER A 303 "
     model   vdw
     1.571 2.450
  nonbonded pdb=" OE2 GLU A 797 "
            pdb=" H1  HOH A2101 "
     model   vdw
     1.582 2.450
  nonbonded pdb="HH22 ARG A  88 "
            pdb=" O   PRO A 609 "
     model   vdw
     1.596 2.450
  nonbonded pdb=" HH  TYR A  24 "
            pdb=" OE1 GLU A  60 "
     model   vdw
     1.602 2.450
  nonbonded pdb=" HG  SER A 350 "
            pdb=" OE1 GLU A 356 "
     model   vdw
     1.617 2.450
  ... (remaining 247594 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=0.12 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.060
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.070
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     22.900
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  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:8.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8935
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      :  0.013   0.289   8568  Z= 0.817
  Angle     :  1.902   8.666  11692  Z= 1.316
  Chirality :  0.105   0.373   1300
  Planarity :  0.017   0.186   1487
  Dihedral  : 13.286  88.045   3156
  Min Nonbonded Distance : 1.832

Molprobity Statistics.
  All-atom Clashscore : 0.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  1.48 %
    Favored  : 98.40 %
  Cbeta Deviations :  0.21 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole: -0.70 (0.23), residues: 1037
  helix: -0.71 (0.21), residues: 457
  sheet:  0.55 (0.52), residues: 89
  loop : -0.23 (0.25), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.002   ARG A 810 
 TYR   0.120   0.025   TYR A 866 
 PHE   0.068   0.013   PHE A 157 
 TRP   0.122   0.020   TRP A 778 
 HIS   0.015   0.003   HIS A  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.01289 ( 8565)
  covalent geometry    : angle       1.90248 (11692)
  hydrogen bonds       : bond        0.22629 (  389)
  hydrogen bonds       : angle       6.83536 ( 1140)
  metal coordination   : bond        0.20539 (    3)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 145
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  497 TYR cc_start: 0.8518 (m-80) cc_final: 0.8230 (m-80)
REVERT: A  714 MET cc_start: 0.9211 (ttm) cc_final: 0.8845 (ttp)
REVERT: A  756 MET cc_start: 0.9352 (tpt) cc_final: 0.8692 (tpt)
REVERT: A  939 MET cc_start: 0.9538 (mtp) cc_final: 0.9080 (mtp)
REVERT: B 1032 ASP cc_start: 0.8679 (m-30) cc_final: 0.8459 (m-30)
  outliers start: 1
  outliers final: 0
  residues processed: 146
  average time/residue: 1.5320
  time to fit residues: 234.0845
Evaluate side-chains
  96 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    0.8980
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.8980
   chunk 100 optimal weight:    0.7980
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 430 GLN
A 639 ASN
A 736 GLN
A 779 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.091097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.068320 restraints weight = 39494.713|
|-----------------------------------------------------------------------------|
r_work (start): 0.2822 rms_B_bonded: 2.06
r_work: 0.2701 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2570 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.2570
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2577
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2577 r_free = 0.2577    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2576 r_free = 0.2576    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2576
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9003
moved from start:          0.2308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.073   8568  Z= 0.182
  Angle     :  0.690   6.530  11692  Z= 0.386
  Chirality :  0.045   0.148   1300
  Planarity :  0.006   0.062   1487
  Dihedral  : 10.786  87.089   1275
  Min Nonbonded Distance : 1.780

Molprobity Statistics.
  All-atom Clashscore : 1.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  6.16 %
    Favored  : 93.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  0.26 (0.25), residues: 1037
  helix:  0.63 (0.24), residues: 469
  sheet:  0.16 (0.41), residues: 118
  loop : -0.16 (0.28), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 746 
 TYR   0.023   0.002   TYR A 527 
 PHE   0.014   0.002   PHE A 137 
 TRP   0.010   0.001   TRP B1075 
 HIS   0.008   0.002   HIS A 655 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 8565)
  covalent geometry    : angle       0.68984 (11692)
  hydrogen bonds       : bond        0.07043 (  389)
  hydrogen bonds       : angle       5.17596 ( 1140)
  metal coordination   : bond        0.00848 (    3)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 98
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  196 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8111 (mp0)
REVERT: A  688 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.7988 (m-30)
REVERT: A  714 MET cc_start: 0.9113 (ttm) cc_final: 0.8767 (ttp)
REVERT: A  747 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8171 (mm-30)
REVERT: A  756 MET cc_start: 0.9325 (tpt) cc_final: 0.8445 (tpt)
REVERT: A  939 MET cc_start: 0.9492 (mtp) cc_final: 0.9057 (mtp)
REVERT: B 1084 ASN cc_start: 0.7559 (p0) cc_final: 0.7356 (p0)
  outliers start: 3
  outliers final: 1
  residues processed: 100
  average time/residue: 1.5810
  time to fit residues: 165.8827
Evaluate side-chains
  90 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 87
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  196 GLU
Chi-restraints excluded: chain A residue  688 ASP
Chi-restraints excluded: chain A residue  744 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 72 optimal weight:    0.0770
   chunk 68 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 70 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9990
   overall best weight:    0.7740

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

Flipped N/Q/H residues before XYZ refinement:
A 300 ASN    A
A 924 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.091407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.068414 restraints weight = 43476.268|
|-----------------------------------------------------------------------------|
r_work (start): 0.2826 rms_B_bonded: 2.15
r_work: 0.2705 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2575 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2575
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2582
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2582 r_free = 0.2582    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2582 r_free = 0.2582    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2582
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8999
moved from start:          0.2684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8568  Z= 0.135
  Angle     :  0.580   5.146  11692  Z= 0.317
  Chirality :  0.042   0.137   1300
  Planarity :  0.005   0.048   1487
  Dihedral  : 10.550  84.075   1275
  Min Nonbonded Distance : 1.811

Molprobity Statistics.
  All-atom Clashscore : 1.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  7.53 %
    Favored  : 91.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  0.67 (0.26), residues: 1037
  helix:  1.18 (0.25), residues: 467
  sheet:  0.16 (0.41), residues: 118
  loop : -0.16 (0.28), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 703 
 TYR   0.019   0.002   TYR A 527 
 PHE   0.011   0.001   PHE A 506 
 TRP   0.010   0.001   TRP A 778 
 HIS   0.010   0.001   HIS A 554 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 8565)
  covalent geometry    : angle       0.57965 (11692)
  hydrogen bonds       : bond        0.05625 (  389)
  hydrogen bonds       : angle       4.71202 ( 1140)
  metal coordination   : bond        0.00399 (    3)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 92
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  714 MET cc_start: 0.9088 (ttm) cc_final: 0.8804 (ttp)
REVERT: A  747 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8194 (mm-30)
REVERT: A  756 MET cc_start: 0.9334 (tpt) cc_final: 0.8704 (tpt)
REVERT: A  939 MET cc_start: 0.9454 (mtp) cc_final: 0.9124 (mtp)
  outliers start: 5
  outliers final: 0
  residues processed: 94
  average time/residue: 1.6928
  time to fit residues: 166.4227
Evaluate side-chains
  87 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 95 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 82 optimal weight:    0.5980
   chunk 3 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 34 optimal weight:    2.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.091458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.068717 restraints weight = 40060.973|
|-----------------------------------------------------------------------------|
r_work (start): 0.2831 rms_B_bonded: 2.06
r_work: 0.2715 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2588 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.2588
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2595
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2595 r_free = 0.2595    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2595 r_free = 0.2595    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2595
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8995
moved from start:          0.2895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8568  Z= 0.129
  Angle     :  0.547   4.989  11692  Z= 0.296
  Chirality :  0.042   0.138   1300
  Planarity :  0.005   0.097   1487
  Dihedral  : 10.445  80.535   1275
  Min Nonbonded Distance : 1.804

Molprobity Statistics.
  All-atom Clashscore : 0.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  7.87 %
    Favored  : 91.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  0.83 (0.26), residues: 1037
  helix:  1.45 (0.25), residues: 467
  sheet:  0.06 (0.42), residues: 118
  loop : -0.19 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 746 
 TYR   0.018   0.002   TYR A 527 
 PHE   0.012   0.001   PHE A 506 
 TRP   0.010   0.001   TRP A 778 
 HIS   0.010   0.001   HIS A 554 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 8565)
  covalent geometry    : angle       0.54680 (11692)
  hydrogen bonds       : bond        0.05075 (  389)
  hydrogen bonds       : angle       4.49862 ( 1140)
  metal coordination   : bond        0.00347 (    3)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 90
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  196 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8128 (mp0)
REVERT: A  714 MET cc_start: 0.9112 (ttm) cc_final: 0.8815 (ttp)
REVERT: A  746 ARG cc_start: 0.8268 (mmt90) cc_final: 0.7940 (mpp80)
REVERT: A  747 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8310 (mm-30)
REVERT: A  756 MET cc_start: 0.9293 (tpt) cc_final: 0.8762 (tpt)
REVERT: A  939 MET cc_start: 0.9422 (mtp) cc_final: 0.9135 (mtp)
  outliers start: 6
  outliers final: 0
  residues processed: 93
  average time/residue: 1.8007
  time to fit residues: 175.4661
Evaluate side-chains
  88 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 87
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  196 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 79 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 99 optimal weight:    4.9990
   chunk 41 optimal weight:    1.9990
   chunk 57 optimal weight:    0.6980
   chunk 24 optimal weight:    0.6980
   chunk 34 optimal weight:    0.7980
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.089846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.067325 restraints weight = 39197.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.2806 rms_B_bonded: 2.04
r_work: 0.2688 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2561 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2561
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2564
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2564 r_free = 0.2564    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2564 r_free = 0.2564    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2564
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9017
moved from start:          0.2975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8568  Z= 0.155
  Angle     :  0.556   4.802  11692  Z= 0.302
  Chirality :  0.042   0.139   1300
  Planarity :  0.006   0.113   1487
  Dihedral  : 10.436  79.282   1275
  Min Nonbonded Distance : 1.742

Molprobity Statistics.
  All-atom Clashscore : 1.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  7.98 %
    Favored  : 91.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  0.72 (0.26), residues: 1037
  helix:  1.40 (0.25), residues: 468
  sheet: -0.13 (0.41), residues: 120
  loop : -0.26 (0.28), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 704 
 TYR   0.019   0.002   TYR A 527 
 PHE   0.013   0.001   PHE A 412 
 TRP   0.010   0.001   TRP A 778 
 HIS   0.009   0.001   HIS A 554 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 8565)
  covalent geometry    : angle       0.55574 (11692)
  hydrogen bonds       : bond        0.05573 (  389)
  hydrogen bonds       : angle       4.52733 ( 1140)
  metal coordination   : bond        0.00498 (    3)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 89
  time to evaluate  : 0.435 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  196 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8028 (mp0)
REVERT: A  714 MET cc_start: 0.9153 (ttm) cc_final: 0.8833 (ttp)
REVERT: A  746 ARG cc_start: 0.8355 (mmt90) cc_final: 0.8041 (mmt90)
REVERT: A  747 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8271 (mm-30)
REVERT: A  756 MET cc_start: 0.9294 (tpt) cc_final: 0.8788 (tpt)
REVERT: A  769 ASP cc_start: 0.8365 (p0) cc_final: 0.8121 (p0)
REVERT: A  864 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8353 (ttp-110)
REVERT: A  939 MET cc_start: 0.9406 (mtp) cc_final: 0.9162 (mtp)
  outliers start: 3
  outliers final: 0
  residues processed: 91
  average time/residue: 1.8636
  time to fit residues: 177.5054
Evaluate side-chains
  88 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 86
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  196 GLU
Chi-restraints excluded: chain A residue  864 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 92 optimal weight:    0.9990
   chunk 80 optimal weight:    0.9980
   chunk 8 optimal weight:    0.2980
   chunk 94 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   overall best weight:    1.0586

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

Flipped N/Q/H residues before XYZ refinement:
A 554 HIS
B1004 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.090883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.067902 restraints weight = 42167.106|
|-----------------------------------------------------------------------------|
r_work (start): 0.2817 rms_B_bonded: 2.12
r_work: 0.2698 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2570 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.2570
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2578
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2578 r_free = 0.2578    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2578 r_free = 0.2578    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2578
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9015
moved from start:          0.3099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8568  Z= 0.137
  Angle     :  0.535   5.324  11692  Z= 0.287
  Chirality :  0.042   0.138   1300
  Planarity :  0.005   0.082   1487
  Dihedral  : 10.417  77.696   1275
  Min Nonbonded Distance : 1.774

Molprobity Statistics.
  All-atom Clashscore : 1.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  :  8.55 %
    Favored  : 90.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  0.78 (0.26), residues: 1037
  helix:  1.51 (0.25), residues: 468
  sheet: -0.13 (0.40), residues: 130
  loop : -0.29 (0.29), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 704 
 TYR   0.016   0.002   TYR A 798 
 PHE   0.011   0.001   PHE A 506 
 TRP   0.010   0.001   TRP A 778 
 HIS   0.008   0.001   HIS A 554 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 8565)
  covalent geometry    : angle       0.53465 (11692)
  hydrogen bonds       : bond        0.05080 (  389)
  hydrogen bonds       : angle       4.43209 ( 1140)
  metal coordination   : bond        0.00297 (    3)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 90
  time to evaluate  : 0.484 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  196 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8045 (mp0)
REVERT: A  714 MET cc_start: 0.9155 (ttm) cc_final: 0.8850 (ttp)
REVERT: A  746 ARG cc_start: 0.8374 (mmt90) cc_final: 0.8076 (mmt90)
REVERT: A  747 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8305 (mm-30)
REVERT: A  756 MET cc_start: 0.9290 (tpt) cc_final: 0.8759 (tpt)
REVERT: A  864 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.8310 (ttp-110)
REVERT: A  939 MET cc_start: 0.9386 (mtp) cc_final: 0.9142 (mtp)
  outliers start: 4
  outliers final: 1
  residues processed: 92
  average time/residue: 2.0352
  time to fit residues: 196.1642
Evaluate side-chains
  88 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 85
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  196 GLU
Chi-restraints excluded: chain A residue  864 ARG
Chi-restraints excluded: chain A residue  964 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 0 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 44 optimal weight:    0.4980
   chunk 76 optimal weight:    0.0570
   chunk 18 optimal weight:    0.7980
   chunk 52 optimal weight:    3.9990
   chunk 85 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 93 optimal weight:    2.9990
   chunk 103 optimal weight:    1.9990
   overall best weight:    1.0702

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

Flipped N/Q/H residues before XYZ refinement:
A 554 HIS
B1004 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.090527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.067920 restraints weight = 39252.425|
|-----------------------------------------------------------------------------|
r_work (start): 0.2818 rms_B_bonded: 2.05
r_work: 0.2700 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2572 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.2572
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2577
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2577 r_free = 0.2577    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2577 r_free = 0.2577    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2577
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9015
moved from start:          0.3138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8568  Z= 0.142
  Angle     :  0.537   5.672  11692  Z= 0.288
  Chirality :  0.042   0.138   1300
  Planarity :  0.006   0.094   1487
  Dihedral  : 10.417  77.164   1275
  Min Nonbonded Distance : 1.768

Molprobity Statistics.
  All-atom Clashscore : 1.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  9.12 %
    Favored  : 90.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  0.80 (0.26), residues: 1037
  helix:  1.53 (0.25), residues: 468
  sheet: -0.11 (0.41), residues: 120
  loop : -0.29 (0.28), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 704 
 TYR   0.018   0.002   TYR A 798 
 PHE   0.011   0.001   PHE A 506 
 TRP   0.010   0.001   TRP A 778 
 HIS   0.008   0.001   HIS A 554 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 8565)
  covalent geometry    : angle       0.53708 (11692)
  hydrogen bonds       : bond        0.05187 (  389)
  hydrogen bonds       : angle       4.43020 ( 1140)
  metal coordination   : bond        0.00379 (    3)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 89
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  196 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8033 (mp0)
REVERT: A  714 MET cc_start: 0.9159 (ttm) cc_final: 0.8865 (ttp)
REVERT: A  746 ARG cc_start: 0.8381 (mmt90) cc_final: 0.8080 (mmt90)
REVERT: A  747 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8290 (mm-30)
REVERT: A  756 MET cc_start: 0.9282 (tpt) cc_final: 0.8762 (tpt)
REVERT: A  769 ASP cc_start: 0.8337 (p0) cc_final: 0.8096 (p0)
REVERT: A  864 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8288 (ttp-110)
REVERT: A  939 MET cc_start: 0.9375 (mtp) cc_final: 0.9120 (mtp)
  outliers start: 3
  outliers final: 1
  residues processed: 91
  average time/residue: 1.7761
  time to fit residues: 169.7163
Evaluate side-chains
  90 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 87
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  196 GLU
Chi-restraints excluded: chain A residue  864 ARG
Chi-restraints excluded: chain A residue  964 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 70 optimal weight:    0.6980
   chunk 46 optimal weight:    0.4980
   chunk 28 optimal weight:    2.9990
   chunk 45 optimal weight:    0.3980
   chunk 82 optimal weight:    0.6980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 554 HIS
B1004 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.091534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.069111 restraints weight = 36632.511|
|-----------------------------------------------------------------------------|
r_work (start): 0.2839 rms_B_bonded: 2.00
r_work: 0.2723 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2598 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.2598
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2605
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2605 r_free = 0.2605    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2605 r_free = 0.2605    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2605
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8997
moved from start:          0.3239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8568  Z= 0.122
  Angle     :  0.519   6.129  11692  Z= 0.276
  Chirality :  0.041   0.138   1300
  Planarity :  0.005   0.094   1487
  Dihedral  : 10.412  75.858   1275
  Min Nonbonded Distance : 1.815

Molprobity Statistics.
  All-atom Clashscore : 1.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  9.12 %
    Favored  : 90.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  0.88 (0.26), residues: 1037
  helix:  1.64 (0.25), residues: 469
  sheet: -0.10 (0.42), residues: 120
  loop : -0.30 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 704 
 TYR   0.014   0.001   TYR A 527 
 PHE   0.011   0.001   PHE A 506 
 TRP   0.010   0.001   TRP A 778 
 HIS   0.007   0.001   HIS A 554 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 8565)
  covalent geometry    : angle       0.51934 (11692)
  hydrogen bonds       : bond        0.04675 (  389)
  hydrogen bonds       : angle       4.33776 ( 1140)
  metal coordination   : bond        0.00254 (    3)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 91
  time to evaluate  : 0.470 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  196 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8057 (mp0)
REVERT: A  714 MET cc_start: 0.9148 (ttm) cc_final: 0.8878 (ttp)
REVERT: A  746 ARG cc_start: 0.8368 (mmt90) cc_final: 0.8066 (mmt90)
REVERT: A  747 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8293 (mm-30)
REVERT: A  756 MET cc_start: 0.9275 (tpt) cc_final: 0.8760 (tpt)
REVERT: A  769 ASP cc_start: 0.8284 (p0) cc_final: 0.7982 (p0)
REVERT: A  864 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.8355 (ttp-110)
REVERT: A  939 MET cc_start: 0.9356 (mtp) cc_final: 0.9058 (mtp)
  outliers start: 3
  outliers final: 1
  residues processed: 93
  average time/residue: 1.7666
  time to fit residues: 172.3081
Evaluate side-chains
  93 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 90
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  196 GLU
Chi-restraints excluded: chain A residue  864 ARG
Chi-restraints excluded: chain A residue  964 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 80 optimal weight:    0.5980
   chunk 77 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 35 optimal weight:    0.6980
   chunk 25 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 554 HIS
B1004 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.091457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.068262 restraints weight = 45817.367|
|-----------------------------------------------------------------------------|
r_work (start): 0.2826 rms_B_bonded: 2.20
r_work: 0.2706 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2578 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.2578
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2582
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2582 r_free = 0.2582    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2582 r_free = 0.2582    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2582
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9010
moved from start:          0.3294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8568  Z= 0.121
  Angle     :  0.528   6.283  11692  Z= 0.280
  Chirality :  0.041   0.137   1300
  Planarity :  0.005   0.095   1487
  Dihedral  : 10.420  75.408   1275
  Min Nonbonded Distance : 1.811

Molprobity Statistics.
  All-atom Clashscore : 1.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  9.24 %
    Favored  : 90.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  0.91 (0.26), residues: 1037
  helix:  1.69 (0.25), residues: 469
  sheet: -0.06 (0.42), residues: 120
  loop : -0.32 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 704 
 TYR   0.015   0.001   TYR A 798 
 PHE   0.011   0.001   PHE A 506 
 TRP   0.010   0.001   TRP A 778 
 HIS   0.007   0.001   HIS A 554 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 8565)
  covalent geometry    : angle       0.52840 (11692)
  hydrogen bonds       : bond        0.04660 (  389)
  hydrogen bonds       : angle       4.32516 ( 1140)
  metal coordination   : bond        0.00266 (    3)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 88
  time to evaluate  : 0.486 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  196 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8074 (mp0)
REVERT: A  714 MET cc_start: 0.9146 (ttm) cc_final: 0.8876 (ttp)
REVERT: A  718 ARG cc_start: 0.8808 (mmm-85) cc_final: 0.8552 (mtt-85)
REVERT: A  746 ARG cc_start: 0.8401 (mmt90) cc_final: 0.8093 (mmt90)
REVERT: A  747 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8327 (mm-30)
REVERT: A  756 MET cc_start: 0.9281 (tpt) cc_final: 0.8774 (tpt)
REVERT: A  769 ASP cc_start: 0.8343 (p0) cc_final: 0.8114 (p0)
REVERT: A  864 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8399 (ttp-110)
REVERT: A  939 MET cc_start: 0.9358 (mtp) cc_final: 0.9066 (mtp)
  outliers start: 3
  outliers final: 1
  residues processed: 90
  average time/residue: 1.8502
  time to fit residues: 174.5446
Evaluate side-chains
  90 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 87
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  196 GLU
Chi-restraints excluded: chain A residue  864 ARG
Chi-restraints excluded: chain A residue  964 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 24 optimal weight:    0.5980
   chunk 87 optimal weight:    2.9990
   chunk 58 optimal weight:    0.0370
   chunk 3 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0970
   chunk 101 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9980
   overall best weight:    0.5458

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

Flipped N/Q/H residues before XYZ refinement:
A 554 HIS
B1004 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.092787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.070229 restraints weight = 39335.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.2859 rms_B_bonded: 2.05
r_work: 0.2745 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2619 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.2619
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2625
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2625 r_free = 0.2625    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2625 r_free = 0.2625    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2625
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8981
moved from start:          0.3396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8568  Z= 0.103
  Angle     :  0.502   6.797  11692  Z= 0.264
  Chirality :  0.040   0.138   1300
  Planarity :  0.005   0.095   1487
  Dihedral  : 10.430  74.061   1275
  Min Nonbonded Distance : 1.866

Molprobity Statistics.
  All-atom Clashscore : 1.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  :  9.24 %
    Favored  : 90.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  1.05 (0.26), residues: 1037
  helix:  1.85 (0.26), residues: 469
  sheet: -0.03 (0.43), residues: 120
  loop : -0.30 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A 704 
 TYR   0.012   0.001   TYR A 527 
 PHE   0.010   0.001   PHE A 506 
 TRP   0.011   0.001   TRP A 778 
 HIS   0.007   0.001   HIS A 554 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 8565)
  covalent geometry    : angle       0.50193 (11692)
  hydrogen bonds       : bond        0.04140 (  389)
  hydrogen bonds       : angle       4.23840 ( 1140)
  metal coordination   : bond        0.00117 (    3)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 91
  time to evaluate  : 0.490 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  196 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8067 (mp0)
REVERT: A  714 MET cc_start: 0.9134 (ttm) cc_final: 0.8886 (ttp)
REVERT: A  718 ARG cc_start: 0.8745 (mmm-85) cc_final: 0.8508 (mtt-85)
REVERT: A  746 ARG cc_start: 0.8369 (mmt90) cc_final: 0.8149 (mpt90)
REVERT: A  747 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8294 (mm-30)
REVERT: A  756 MET cc_start: 0.9258 (tpt) cc_final: 0.8777 (tpt)
REVERT: A  769 ASP cc_start: 0.8241 (p0) cc_final: 0.7933 (p0)
REVERT: A  864 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8358 (ttp-110)
REVERT: A  939 MET cc_start: 0.9339 (mtp) cc_final: 0.9053 (mtp)
  outliers start: 4
  outliers final: 1
  residues processed: 93
  average time/residue: 1.9209
  time to fit residues: 187.3005
Evaluate side-chains
  90 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 87
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  196 GLU
Chi-restraints excluded: chain A residue  864 ARG
Chi-restraints excluded: chain A residue  964 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 53 optimal weight:    0.2980
   chunk 67 optimal weight:    0.9980
   chunk 76 optimal weight:    1.9990
   chunk 83 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9980
   chunk 93 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 101 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 64 optimal weight:    3.9990
   chunk 37 optimal weight:    0.4980
   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 554 HIS
A 639 ASN
B1004 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.092120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.069590 restraints weight = 39475.927|
|-----------------------------------------------------------------------------|
r_work (start): 0.2849 rms_B_bonded: 2.05
r_work: 0.2734 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2609 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.2609
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2613
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2613 r_free = 0.2613    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2613 r_free = 0.2613    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2613
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8990
moved from start:          0.3393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8568  Z= 0.115
  Angle     :  0.515   6.591  11692  Z= 0.271
  Chirality :  0.040   0.136   1300
  Planarity :  0.005   0.094   1487
  Dihedral  : 10.430  73.744   1275
  Min Nonbonded Distance : 1.823

Molprobity Statistics.
  All-atom Clashscore : 1.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  9.69 %
    Favored  : 89.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  1.03 (0.26), residues: 1037
  helix:  1.82 (0.26), residues: 469
  sheet: -0.01 (0.43), residues: 120
  loop : -0.29 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 704 
 TYR   0.015   0.001   TYR A 798 
 PHE   0.011   0.001   PHE A 506 
 TRP   0.010   0.001   TRP A 778 
 HIS   0.007   0.001   HIS A 554 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 8565)
  covalent geometry    : angle       0.51530 (11692)
  hydrogen bonds       : bond        0.04401 (  389)
  hydrogen bonds       : angle       4.25870 ( 1140)
  metal coordination   : bond        0.00254 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7419.91 seconds
wall clock time: 125 minutes 48.04 seconds (7548.04 seconds total)