Starting phenix.real_space_refine
on Fri Jul  3 09:42:06 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rkt_19282/07_2026/8rkt_19282.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rkt_19282/07_2026/8rkt_19282.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.35
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8rkt_19282/07_2026/8rkt_19282.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rkt_19282/07_2026/8rkt_19282.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rkt_19282/07_2026/8rkt_19282.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rkt_19282/07_2026/8rkt_19282.cif"
  }
  resolution = 2.35
  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
-------------------------------------------------------------------------------
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=   0.002 sd=   0.075
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      2      6.06       5
     P     310      5.49       5
     Mg      1      5.21       5
     S      30      5.16       5
     C    7329      2.51       5
     N    2427      2.21       5
     O    3695      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 13794
  Number of models: 1
  Model: ""
    Number of chains: 14
    Chain: "1"
      Number of atoms: 5239
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 246, 5239
          Classifications: {'RNA': 246}
          Modifications used: {'5*END': 1, 'rna2p_pur': 21, 'rna2p_pyr': 17, 'rna3p_pur': 107, 'rna3p_pyr': 101}
          Link IDs: {'rna2p': 38, 'rna3p': 207}
    Chain: "2"
      Number of atoms: 696
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 696
          Classifications: {'DNA': 34}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 33}
    Chain: "3"
      Number of atoms: 647
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 647
          Classifications: {'DNA': 32}
          Link IDs: {'rna3p': 31}
    Chain: "A"
      Number of atoms: 4872
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 602, 4872
          Classifications: {'peptide': 602}
          Link IDs: {'PTRANS': 18, 'TRANS': 583}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 708
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 87, 708
          Classifications: {'peptide': 87}
          Link IDs: {'TRANS': 86}
    Chain: "C"
      Number of atoms: 1306
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 164, 1306
          Classifications: {'peptide': 164}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 150}
    Chain: "1"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "1"
      Number of atoms: 160
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 160, 160
          Classifications: {'water': 160}
          Link IDs: {None: 159}
    Chain: "2"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 7
          Classifications: {'water': 7}
          Link IDs: {None: 6}
    Chain: "3"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 33
          Classifications: {'water': 33}
          Link IDs: {None: 32}
    Chain: "A"
      Number of atoms: 93
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 93
          Classifications: {'water': 93}
          Link IDs: {None: 92}
    Chain: "B"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 13
          Classifications: {'water': 13}
          Link IDs: {None: 12}
    Chain: "C"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 17
          Classifications: {'water': 17}
          Link IDs: {None: 16}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  13205  SG  CYS C 133      40.436 123.263  33.806  1.00 30.64           S
  ATOM  13226  SG  CYS C 136      38.341 120.320  32.674  1.00 34.07           S
  ATOM  13342  SG  CYS C 151      41.754 120.712  31.254  1.00 40.26           S
  ATOM  13369  SG  CYS C 154      39.055 123.236  30.327  1.00 46.87           S
  ATOM  12930  SG  CYS C 100      51.117 131.217  40.191  1.00 34.05           S
  ATOM  12945  SG  CYS C 103      54.710 131.386  39.195  1.00 29.68           S
  ATOM  13114  SG  CYS C 122      53.673 132.699  42.623  1.00 35.65           S

  Time building chain proxies: 3.12, per 1000 atoms: 0.23
  Number of scatterers: 13794
  At special positions: 0
  Unit cell: (116.48, 144.144, 117.936, 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      2     29.99
     S      30     16.00
     P     310     15.00
     Mg      1     11.99
     O    3695      8.00
     N    2427      7.00
     C    7329      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.19
  Conformation dependent library (CDL) restraints added in 524.9 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN C 200 "
        pdb="ZN    ZN C 200 " - pdb=" SG  CYS C 136 "
        pdb="ZN    ZN C 200 " - pdb=" SG  CYS C 133 "
        pdb="ZN    ZN C 200 " - pdb=" SG  CYS C 151 "
        pdb="ZN    ZN C 200 " - pdb=" SG  CYS C 154 "
      pdb="  ZN C 201 "
        pdb="ZN    ZN C 201 " - pdb=" ND1 HIS C 125 "
        pdb="ZN    ZN C 201 " - pdb=" SG  CYS C 100 "
        pdb="ZN    ZN C 201 " - pdb=" SG  CYS C 103 "
        pdb="ZN    ZN C 201 " - pdb=" SG  CYS C 122 "
      Number of angles added : 9


  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1616

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 3 sheets defined
      62.8% alpha, 7.9% beta
      109 base pairs and 188 stacking pairs defined.
    Time for finding SS restraints: 2.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 27
    Processing helix  chain 'A' and resid 27 through 40
    Processing helix  chain 'A' and resid 44 through 52
      removed outlier: 3.532A  pdb=" N   GLN A  50 " --> pdb=" O   GLU A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 57 through 67
      Proline residue:  A  65  - end of helix
    Processing helix  chain 'A' and resid 76 through 115
    Processing helix  chain 'A' and resid 117 through 126
      removed outlier: 3.730A  pdb=" N   GLU A 123 " --> pdb=" O   ALA A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 144
    Processing helix  chain 'A' and resid 174 through 185
      removed outlier: 3.641A  pdb=" N   GLN A 183 " --> pdb=" O   PHE A 179 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   GLU A 184 " --> pdb=" O   ASP A 180 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   THR A 185 " --> pdb=" O   ALA A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 200
      removed outlier: 3.531A  pdb=" N   ASN A 200 " --> pdb=" O   TYR A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 232
    Processing helix  chain 'A' and resid 244 through 257
      removed outlier: 3.500A  pdb=" N   LEU A 248 " --> pdb=" O   ASN A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 261 through 274
    Processing helix  chain 'A' and resid 287 through 289
      No H-bonds generated for 'chain 'A' and resid 287 through 289'
    Processing helix  chain 'A' and resid 318 through 338
      removed outlier: 4.167A  pdb=" N   HIS A 323 " --> pdb=" O   ASN A 319 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   TRP A 324 " --> pdb=" O   ARG A 320 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   PHE A 325 " --> pdb=" O   GLN A 321 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   LEU A 329 " --> pdb=" O   PHE A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 347
    Processing helix  chain 'A' and resid 364 through 369
    Processing helix  chain 'A' and resid 380 through 382
      No H-bonds generated for 'chain 'A' and resid 380 through 382'
    Processing helix  chain 'A' and resid 383 through 406
      removed outlier: 3.583A  pdb=" N   LYS A 406 " --> pdb=" O   ILE A 402 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 429
    Processing helix  chain 'A' and resid 476 through 482
    Processing helix  chain 'A' and resid 485 through 508
      removed outlier: 4.086A  pdb=" N   ASN A 489 " --> pdb=" O   TYR A 485 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   LYS A 507 " --> pdb=" O   HIS A 503 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ASN A 508 " --> pdb=" O   LYS A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 516 through 538
    Processing helix  chain 'A' and resid 550 through 567
      removed outlier: 3.600A  pdb=" N   GLN A 565 " --> pdb=" O   ALA A 561 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 570 through 577
    Processing helix  chain 'A' and resid 578 through 588
    Processing helix  chain 'A' and resid 589 through 604
    Processing helix  chain 'A' and resid 618 through 633
    Processing helix  chain 'B' and resid 5 through 17
    Processing helix  chain 'B' and resid 25 through 47
      removed outlier: 3.566A  pdb=" N   ALA B  46 " --> pdb=" O   LEU B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 73
      removed outlier: 3.641A  pdb=" N   GLY B  56 " --> pdb=" O   SER B  52 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   LYS B  73 " --> pdb=" O   ALA B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 75 through 87
    Processing helix  chain 'C' and resid 21 through 33
    Processing helix  chain 'C' and resid 36 through 45
    Processing helix  chain 'C' and resid 48 through 55
      removed outlier: 3.568A  pdb=" N   ARG C  52 " --> pdb=" O   ALA C  48 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ARG C  55 " --> pdb=" O   ALA C  51 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 63 through 74
      removed outlier: 3.841A  pdb=" N   VAL C  73 " --> pdb=" O   ALA C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 77 through 83
    Processing helix  chain 'C' and resid 111 through 116
    Processing helix  chain 'C' and resid 142 through 146
    Processing helix  chain 'C' and resid 159 through 165
      removed outlier: 3.544A  pdb=" N   ALA C 162 " --> pdb=" O   ALA C 159 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   GLN C 165 " --> pdb=" O   ALA C 162 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 283 through 285
      removed outlier: 6.562A  pdb=" N   LEU A 349 " --> pdb=" O   ASP A 378 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   ASP A 378 " --> pdb=" O   LEU A 349 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ASN A 351 " --> pdb=" O   CYS A 376 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   LEU A 371 " --> pdb=" O   LEU A  10 " (cutoff:3.500A)
      removed outlier: 5.169A  pdb=" N   LEU A 301 " --> pdb=" O   VAL A 315 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 470 through 475
      removed outlier: 6.558A  pdb=" N   VAL A 463 " --> pdb=" O   LEU A 472 " (cutoff:3.500A)
      removed outlier: 4.535A  pdb=" N   TYR A 474 " --> pdb=" O   VAL A 461 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   VAL A 461 " --> pdb=" O   TYR A 474 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   SER A 445 " --> pdb=" O   ALA A 540 " (cutoff:3.500A)
      removed outlier: 6.011A  pdb=" N   SER A 542 " --> pdb=" O   SER A 445 " (cutoff:3.500A)
      removed outlier: 7.118A  pdb=" N   ILE A 447 " --> pdb=" O   SER A 542 " (cutoff:3.500A)
      removed outlier: 8.026A  pdb=" N   VAL A 544 " --> pdb=" O   ILE A 447 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   VAL A 449 " --> pdb=" O   VAL A 544 " (cutoff:3.500A)
      removed outlier: 8.939A  pdb=" N   VAL A 451 " --> pdb=" O   PRO A 546 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 121 through 122

    404 hydrogen bonds defined for protein.
    1164 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      277 hydrogen bonds
      522 hydrogen bond angles
      0 basepair planarities
      109 basepair parallelities
      188 stacking parallelities
  Total time for adding SS restraints: 2.95

  Time building geometry restraints manager: 1.62 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1889
        1.32 -     1.45: 5358
        1.45 -     1.57: 6467
        1.57 -     1.69: 619
        1.69 -     1.81: 44
  Bond restraints: 14377
  Sorted by residual:
  bond pdb=" C3'  DA 3 126 "
       pdb=" O3'  DA 3 126 "
    ideal  model  delta    sigma   weight residual
    1.435  1.373  0.062 1.30e-02 5.92e+03 2.31e+01
  bond pdb=" C3'  DG 2   6 "
       pdb=" C2'  DG 2   6 "
    ideal  model  delta    sigma   weight residual
    1.516  1.554 -0.038 8.00e-03 1.56e+04 2.25e+01
  bond pdb=" C3'  DC 3 106 "
       pdb=" C2'  DC 3 106 "
    ideal  model  delta    sigma   weight residual
    1.516  1.551 -0.035 8.00e-03 1.56e+04 1.93e+01
  bond pdb=" C3'  DG 3 104 "
       pdb=" C2'  DG 3 104 "
    ideal  model  delta    sigma   weight residual
    1.516  1.545 -0.029 8.00e-03 1.56e+04 1.35e+01
  bond pdb=" C3'  DC 2  12 "
       pdb=" C2'  DC 2  12 "
    ideal  model  delta    sigma   weight residual
    1.516  1.545 -0.029 8.00e-03 1.56e+04 1.32e+01
  ... (remaining 14372 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.29: 20071
        2.29 -     4.58: 764
        4.58 -     6.86: 58
        6.86 -     9.15: 4
        9.15 -    11.44: 1
  Bond angle restraints: 20898
  Sorted by residual:
  angle pdb=" C3'  DT 3 130 "
        pdb=" O3'  DT 3 130 "
        pdb=" P    DC 3 131 "
      ideal   model   delta    sigma   weight residual
     120.20  108.76   11.44 1.50e+00 4.44e-01 5.82e+01
  angle pdb=" O5'  DC 2  29 "
        pdb=" C5'  DC 2  29 "
        pdb=" C4'  DC 2  29 "
      ideal   model   delta    sigma   weight residual
     109.40  115.11   -5.71 8.00e-01 1.56e+00 5.10e+01
  angle pdb=" O4'  DC 2  10 "
        pdb=" C4'  DC 2  10 "
        pdb=" C3'  DC 2  10 "
      ideal   model   delta    sigma   weight residual
     106.00  101.74    4.26 6.00e-01 2.78e+00 5.05e+01
  angle pdb=" O4'  DA 3 126 "
        pdb=" C1'  DA 3 126 "
        pdb=" N9   DA 3 126 "
      ideal   model   delta    sigma   weight residual
     108.00  112.46   -4.46 7.00e-01 2.04e+00 4.07e+01
  angle pdb=" O4'  DA 2  31 "
        pdb=" C1'  DA 2  31 "
        pdb=" N9   DA 2  31 "
      ideal   model   delta    sigma   weight residual
     108.00  112.39   -4.39 7.00e-01 2.04e+00 3.94e+01
  ... (remaining 20893 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.96: 8063
       35.96 -    71.91: 729
       71.91 -   107.87: 37
      107.87 -   143.82: 6
      143.82 -   179.78: 7
  Dihedral angle restraints: 8842
    sinusoidal: 6355
      harmonic: 2487
  Sorted by residual:
  dihedral pdb=" O4'   U 1 170 "
           pdb=" C1'   U 1 170 "
           pdb=" N1    U 1 170 "
           pdb=" C2    U 1 170 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   33.10  166.90     1      1.50e+01 4.44e-03 8.42e+01
  dihedral pdb=" O4'   U 1  41 "
           pdb=" C1'   U 1  41 "
           pdb=" N1    U 1  41 "
           pdb=" C2    U 1  41 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   36.46  163.54     1      1.50e+01 4.44e-03 8.36e+01
  dihedral pdb=" O4'   U 1  39 "
           pdb=" C1'   U 1  39 "
           pdb=" N1    U 1  39 "
           pdb=" C2    U 1  39 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   38.24  161.76     1      1.50e+01 4.44e-03 8.32e+01
  ... (remaining 8839 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.124: 2333
       0.124 -    0.249: 170
       0.249 -    0.373: 16
       0.373 -    0.498: 3
       0.498 -    0.622: 2
  Chirality restraints: 2524
  Sorted by residual:
  chirality pdb=" C3'   A 1 196 "
            pdb=" C4'   A 1 196 "
            pdb=" O3'   A 1 196 "
            pdb=" C2'   A 1 196 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.12   -0.62 2.00e-01 2.50e+01 9.67e+00
  chirality pdb=" C3'  DA 2   5 "
            pdb=" C4'  DA 2   5 "
            pdb=" O3'  DA 2   5 "
            pdb=" C2'  DA 2   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.17   -0.56 2.00e-01 2.50e+01 7.88e+00
  chirality pdb=" P    DT 3 129 "
            pdb=" OP1  DT 3 129 "
            pdb=" OP2  DT 3 129 "
            pdb=" O5'  DT 3 129 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.80   -0.46 2.00e-01 2.50e+01 5.33e+00
  ... (remaining 2521 not shown)

  Planarity restraints: 1532
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C 1  99 "    0.084 2.00e-02 2.50e+03   4.90e-02 5.41e+01
        pdb=" N1    C 1  99 "   -0.074 2.00e-02 2.50e+03
        pdb=" C2    C 1  99 "   -0.024 2.00e-02 2.50e+03
        pdb=" O2    C 1  99 "    0.004 2.00e-02 2.50e+03
        pdb=" N3    C 1  99 "    0.002 2.00e-02 2.50e+03
        pdb=" C4    C 1  99 "    0.004 2.00e-02 2.50e+03
        pdb=" N4    C 1  99 "    0.013 2.00e-02 2.50e+03
        pdb=" C5    C 1  99 "    0.059 2.00e-02 2.50e+03
        pdb=" C6    C 1  99 "   -0.068 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U 1 127 "   -0.079 2.00e-02 2.50e+03   4.75e-02 5.08e+01
        pdb=" N1    U 1 127 "    0.074 2.00e-02 2.50e+03
        pdb=" C2    U 1 127 "    0.002 2.00e-02 2.50e+03
        pdb=" O2    U 1 127 "    0.005 2.00e-02 2.50e+03
        pdb=" N3    U 1 127 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4    U 1 127 "   -0.007 2.00e-02 2.50e+03
        pdb=" O4    U 1 127 "   -0.008 2.00e-02 2.50e+03
        pdb=" C5    U 1 127 "   -0.057 2.00e-02 2.50e+03
        pdb=" C6    U 1 127 "    0.072 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C 1 245 "    0.063 2.00e-02 2.50e+03   3.96e-02 3.52e+01
        pdb=" N1    C 1 245 "   -0.051 2.00e-02 2.50e+03
        pdb=" C2    C 1 245 "    0.006 2.00e-02 2.50e+03
        pdb=" O2    C 1 245 "   -0.011 2.00e-02 2.50e+03
        pdb=" N3    C 1 245 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4    C 1 245 "    0.003 2.00e-02 2.50e+03
        pdb=" N4    C 1 245 "    0.006 2.00e-02 2.50e+03
        pdb=" C5    C 1 245 "    0.053 2.00e-02 2.50e+03
        pdb=" C6    C 1 245 "   -0.068 2.00e-02 2.50e+03
  ... (remaining 1529 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 240
        2.62 -     3.19: 11521
        3.19 -     3.76: 26435
        3.76 -     4.33: 36697
        4.33 -     4.90: 50343
  Nonbonded interactions: 125236
  Sorted by model distance:
  nonbonded pdb="MG    MG 1 300 "
            pdb=" O   HOH 1 447 "
     model   vdw
     2.046 2.170
  nonbonded pdb="MG    MG 1 300 "
            pdb=" O   HOH C 317 "
     model   vdw
     2.056 2.170
  nonbonded pdb="MG    MG 1 300 "
            pdb=" O   HOH 1 492 "
     model   vdw
     2.058 2.170
  nonbonded pdb="MG    MG 1 300 "
            pdb=" O   HOH 1 527 "
     model   vdw
     2.071 2.170
  nonbonded pdb=" OP1   A 1 173 "
            pdb="MG    MG 1 300 "
     model   vdw
     2.185 2.170
  ... (remaining 125231 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=1.00 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:                  0.010
  Normalize map: mean=0, sd=1:             2.450
  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:             0.000
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     17.290
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8502
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      :  0.006   0.062  14385  Z= 0.480
  Angle     :  0.975  11.440  20907  Z= 0.767
  Chirality :  0.073   0.622   2524
  Planarity :  0.012   0.118   1532
  Dihedral  : 22.001 179.780   7226
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 3.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.24 (0.26), residues: 843
  helix: -0.20 (0.20), residues: 493
  sheet:  0.11 (0.63), residues: 62
  loop :  0.22 (0.37), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.004   ARG A 490 
 TYR   0.022   0.005   TYR A  91 
 PHE   0.027   0.003   PHE A  13 
 TRP   0.021   0.003   TRP A  94 
 HIS   0.015   0.002   HIS A 353 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00600 /  0.48 (14377)
  covalent geometry    : angle       0.97495 /  0.77 (20898)
  hydrogen bonds       : bond        0.13813 / 13.75 (  681)
  hydrogen bonds       : angle       5.42584 /  6.24 ( 1686)
  metal coordination   : bond        0.02466 /  1.64 (    8)
  metal coordination   : angle       1.85305 /  3.48 (    9)

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.366 
Fit side-chains
REVERT: A   24 MET cc_start: 0.9093 (mtp) cc_final: 0.8777 (mtp)
REVERT: A  226 GLN cc_start: 0.8022 (tt0) cc_final: 0.7812 (tm-30)
REVERT: A  252 LEU cc_start: 0.8776 (mt) cc_final: 0.8568 (mp)
REVERT: A  260 GLU cc_start: 0.7600 (pt0) cc_final: 0.7381 (pt0)
REVERT: A  267 ARG cc_start: 0.8076 (mtm110) cc_final: 0.7866 (mtp180)
REVERT: A  397 GLU cc_start: 0.8185 (tt0) cc_final: 0.7877 (tt0)
REVERT: A  416 GLN cc_start: 0.7708 (tp40) cc_final: 0.7398 (tp-100)
REVERT: A  496 GLN cc_start: 0.8474 (mt0) cc_final: 0.8251 (mt0)
REVERT: A  612 LYS cc_start: 0.7488 (tppt) cc_final: 0.7067 (ttpt)
REVERT: A  621 ASP cc_start: 0.7717 (t0) cc_final: 0.7500 (t70)
REVERT: B    9 LYS cc_start: 0.6910 (ttpt) cc_final: 0.6095 (ttpt)
REVERT: C   93 GLN cc_start: 0.8254 (mt0) cc_final: 0.7264 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.9503
  time to fit residues: 126.8986
Evaluate side-chains
  101 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    9.9990
   chunk 49 optimal weight:    8.9990
   chunk 97 optimal weight:    4.9990
   chunk 113 optimal weight:    0.0000
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:   20.0000
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    7.9990
   chunk 100 optimal weight:    2.9990
   overall best weight:    3.1992

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 423 GLN
A 431 ASN
B  10 GLN
B  80 GLN
C 135 ASN
C 137 GLN
C 165 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.178275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.135976 restraints weight = 12219.666|
|-----------------------------------------------------------------------------|
r_work (start): 0.3530 rms_B_bonded: 0.79
r_work: 0.3316 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3214 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8687
moved from start:          0.1145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  14385  Z= 0.179
  Angle     :  0.632   6.863  20907  Z= 0.383
  Chirality :  0.047   0.340   2524
  Planarity :  0.005   0.033   1532
  Dihedral  : 23.927 178.755   5469
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  :  7.13 %
    Favored  : 91.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.47 (0.29), residues: 843
  helix:  1.29 (0.22), residues: 503
  sheet:  0.81 (0.66), residues: 65
  loop :  0.65 (0.40), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 490 
 TYR   0.024   0.002   TYR A  91 
 PHE   0.022   0.002   PHE A 214 
 TRP   0.012   0.002   TRP A  21 
 HIS   0.007   0.001   HIS A 353 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00329 /  0.18 (14377)
  covalent geometry    : angle       0.63054 /  0.38 (20898)
  hydrogen bonds       : bond        0.05870 /  5.83 (  681)
  hydrogen bonds       : angle       3.70170 /  4.29 ( 1686)
  metal coordination   : bond        0.01374 /  0.92 (    8)
  metal coordination   : angle       2.46805 /  4.49 (    9)

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 99
  time to evaluate  : 0.364 
Fit side-chains
REVERT: A   24 MET cc_start: 0.8994 (mtp) cc_final: 0.8768 (mtp)
REVERT: A  252 LEU cc_start: 0.8707 (mt) cc_final: 0.8471 (mp)
REVERT: A  341 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7596 (mp-120)
REVERT: A  416 GLN cc_start: 0.7746 (tp40) cc_final: 0.7541 (tp-100)
REVERT: A  566 LYS cc_start: 0.8248 (tttp) cc_final: 0.8005 (ttmp)
REVERT: B    9 LYS cc_start: 0.7105 (ttpt) cc_final: 0.6622 (ttpt)
REVERT: C   93 GLN cc_start: 0.8477 (mt0) cc_final: 0.7236 (pm20)
  outliers start: 9
  outliers final: 3
  residues processed: 100
  average time/residue: 0.8747
  time to fit residues: 92.9695
Evaluate side-chains
  96 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 92
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 LYS
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  341 GLN
Chi-restraints excluded: chain C residue   73 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 87 optimal weight:    4.9990
   chunk 50 optimal weight:    9.9990
   chunk 82 optimal weight:    5.9990
   chunk 92 optimal weight:    5.9990
   chunk 51 optimal weight:    5.9990
   chunk 28 optimal weight:   10.0000
   chunk 52 optimal weight:    6.9990
   chunk 91 optimal weight:    7.9990
   chunk 78 optimal weight:    0.9990
   chunk 47 optimal weight:    0.0060
   chunk 18 optimal weight:   20.0000
   overall best weight:    3.6004

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 423 GLN
A 620 HIS
B  80 GLN
C 137 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.177287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.134603 restraints weight = 12248.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.3513 rms_B_bonded: 0.80
r_work: 0.3296 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3197 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8700
moved from start:          0.1508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  14385  Z= 0.181
  Angle     :  0.597   6.350  20907  Z= 0.361
  Chirality :  0.045   0.341   2524
  Planarity :  0.004   0.037   1532
  Dihedral  : 23.908 177.414   5469
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  :  8.61 %
    Favored  : 89.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.75 (0.29), residues: 843
  helix:  1.60 (0.23), residues: 504
  sheet:  0.79 (0.66), residues: 65
  loop :  0.63 (0.40), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 552 
 TYR   0.021   0.002   TYR A  91 
 PHE   0.023   0.002   PHE A  13 
 TRP   0.011   0.002   TRP A 382 
 HIS   0.009   0.001   HIS A 353 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00336 /  0.18 (14377)
  covalent geometry    : angle       0.59540 /  0.36 (20898)
  hydrogen bonds       : bond        0.05569 /  5.55 (  681)
  hydrogen bonds       : angle       3.51567 /  4.12 ( 1686)
  metal coordination   : bond        0.01148 /  0.77 (    8)
  metal coordination   : angle       2.27085 /  4.15 (    9)

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 0.361 
Fit side-chains
REVERT: A  252 LEU cc_start: 0.8724 (mt) cc_final: 0.8484 (mp)
REVERT: A  341 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7650 (mp-120)
REVERT: A  566 LYS cc_start: 0.8241 (tttp) cc_final: 0.7960 (ttmp)
REVERT: B    9 LYS cc_start: 0.7158 (ttpt) cc_final: 0.6598 (ttpt)
REVERT: C   93 GLN cc_start: 0.8533 (mt0) cc_final: 0.7265 (pm20)
REVERT: C  161 MET cc_start: 0.8592 (mtm) cc_final: 0.8377 (mtt)
  outliers start: 12
  outliers final: 4
  residues processed: 95
  average time/residue: 0.9124
  time to fit residues: 91.6888
Evaluate side-chains
  97 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 92
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 LYS
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  341 GLN
Chi-restraints excluded: chain A residue  438 GLN
Chi-restraints excluded: chain C residue   73 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 10 optimal weight:   20.0000
   chunk 79 optimal weight:    6.9990
   chunk 82 optimal weight:    8.9990
   chunk 67 optimal weight:   10.0000
   chunk 23 optimal weight:   10.0000
   chunk 44 optimal weight:   10.0000
   chunk 76 optimal weight:   10.0000
   chunk 24 optimal weight:   20.0000
   chunk 4 optimal weight:   30.0000
   chunk 74 optimal weight:    5.9990
   chunk 19 optimal weight:   20.0000
   overall best weight:    8.3994

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 423 GLN
A 431 ASN
A 500 HIS
A 620 HIS
B  80 GLN
C 135 ASN
C 137 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.173396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.130883 restraints weight = 12174.195|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 1.07
r_work: 0.3245 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3145 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8736
moved from start:          0.1670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057  14385  Z= 0.323
  Angle     :  0.767   8.249  20907  Z= 0.437
  Chirality :  0.055   0.419   2524
  Planarity :  0.006   0.056   1532
  Dihedral  : 24.045 178.722   5469
  Min Nonbonded Distance : 1.849

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 10.50 %
    Favored  : 87.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.20 (0.28), residues: 843
  helix:  1.14 (0.22), residues: 502
  sheet:  0.29 (0.64), residues: 62
  loop :  0.51 (0.39), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  89 
 TYR   0.029   0.003   TYR A  91 
 PHE   0.027   0.003   PHE A  13 
 TRP   0.017   0.003   TRP A 382 
 HIS   0.007   0.002   HIS C  24 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00646 /  0.32 (14377)
  covalent geometry    : angle       0.76483 /  0.44 (20898)
  hydrogen bonds       : bond        0.06769 /  6.70 (  681)
  hydrogen bonds       : angle       3.72423 /  4.35 ( 1686)
  metal coordination   : bond        0.01940 /  1.29 (    8)
  metal coordination   : angle       3.08481 /  5.67 (    9)

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.337 
Fit side-chains
REVERT: A  275 ARG cc_start: 0.7610 (tmm160) cc_final: 0.6968 (tpp80)
REVERT: A  341 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7680 (mp-120)
REVERT: B    9 LYS cc_start: 0.7251 (ttpt) cc_final: 0.6639 (ttpt)
REVERT: B   89 ARG cc_start: 0.7704 (mtm-85) cc_final: 0.7485 (mtm180)
REVERT: C   93 GLN cc_start: 0.8654 (mt0) cc_final: 0.7288 (pm20)
  outliers start: 13
  outliers final: 7
  residues processed: 101
  average time/residue: 0.9422
  time to fit residues: 100.5358
Evaluate side-chains
  103 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 LYS
Chi-restraints excluded: chain A residue  246 LYS
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  339 LYS
Chi-restraints excluded: chain A residue  341 GLN
Chi-restraints excluded: chain A residue  438 GLN
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  163 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 21 optimal weight:   50.0000
   chunk 64 optimal weight:    2.9990
   chunk 36 optimal weight:    4.9990
   chunk 9 optimal weight:   20.0000
   chunk 20 optimal weight:   50.0000
   chunk 58 optimal weight:    6.9990
   chunk 76 optimal weight:    6.9990
   chunk 98 optimal weight:    0.0070
   chunk 32 optimal weight:    0.9990
   chunk 27 optimal weight:   30.0000
   chunk 88 optimal weight:    5.9990
   overall best weight:    3.0006

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 431 ASN
A 620 HIS
B  80 GLN
C 137 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.177109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.134463 restraints weight = 12230.983|
|-----------------------------------------------------------------------------|
r_work (start): 0.3510 rms_B_bonded: 0.77
r_work: 0.3298 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3198 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8694
moved from start:          0.1784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  14385  Z= 0.166
  Angle     :  0.580   8.027  20907  Z= 0.350
  Chirality :  0.043   0.317   2524
  Planarity :  0.004   0.034   1532
  Dihedral  : 24.008 177.981   5469
  Min Nonbonded Distance : 1.943

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 10.77 %
    Favored  : 87.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.63 (0.29), residues: 843
  helix:  1.57 (0.23), residues: 504
  sheet:  0.69 (0.66), residues: 65
  loop :  0.43 (0.39), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  89 
 TYR   0.016   0.002   TYR A  91 
 PHE   0.020   0.002   PHE A 214 
 TRP   0.012   0.001   TRP A 382 
 HIS   0.005   0.001   HIS A 620 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00303 /  0.17 (14377)
  covalent geometry    : angle       0.57808 /  0.35 (20898)
  hydrogen bonds       : bond        0.05264 /  5.24 (  681)
  hydrogen bonds       : angle       3.47898 /  4.09 ( 1686)
  metal coordination   : bond        0.00969 /  0.65 (    8)
  metal coordination   : angle       2.48852 /  4.62 (    9)

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 94
  time to evaluate  : 0.370 
Fit side-chains
REVERT: A  336 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7670 (mtt180)
REVERT: A  341 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7670 (mp-120)
REVERT: A  477 ILE cc_start: 0.9015 (OUTLIER) cc_final: 0.8742 (tp)
REVERT: A  566 LYS cc_start: 0.8262 (tttp) cc_final: 0.7941 (ttmp)
REVERT: B    9 LYS cc_start: 0.7162 (ttpt) cc_final: 0.6509 (ttpt)
REVERT: B   15 ASN cc_start: 0.8056 (OUTLIER) cc_final: 0.7584 (t0)
REVERT: B   89 ARG cc_start: 0.7638 (mtm-85) cc_final: 0.7434 (mtm180)
REVERT: C   93 GLN cc_start: 0.8574 (mt0) cc_final: 0.7231 (pm20)
  outliers start: 15
  outliers final: 2
  residues processed: 100
  average time/residue: 1.0003
  time to fit residues: 105.8133
Evaluate side-chains
  98 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 92
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 LYS
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  341 GLN
Chi-restraints excluded: chain A residue  477 ILE
Chi-restraints excluded: chain B residue   15 ASN
Chi-restraints excluded: chain C residue   73 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 45 optimal weight:    0.0970
   chunk 27 optimal weight:   30.0000
   chunk 71 optimal weight:    7.9990
   chunk 46 optimal weight:    8.9990
   chunk 93 optimal weight:    1.9990
   chunk 62 optimal weight:    8.9990
   chunk 83 optimal weight:    2.9990
   chunk 106 optimal weight:   10.0000
   chunk 36 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 75 optimal weight:    3.9990
   overall best weight:    2.2186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 431 ASN
A 620 HIS
B  47 ASN
B  80 GLN
C 135 ASN
C 137 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.178591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.136274 restraints weight = 12182.047|
|-----------------------------------------------------------------------------|
r_work (start): 0.3533 rms_B_bonded: 0.83
r_work: 0.3320 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3219 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8668
moved from start:          0.1954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  14385  Z= 0.143
  Angle     :  0.536   7.427  20907  Z= 0.328
  Chirality :  0.041   0.305   2524
  Planarity :  0.004   0.035   1532
  Dihedral  : 23.937 178.320   5469
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 11.44 %
    Favored  : 86.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.93 (0.29), residues: 843
  helix:  1.84 (0.23), residues: 504
  sheet:  0.71 (0.68), residues: 65
  loop :  0.51 (0.39), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  89 
 TYR   0.016   0.002   TYR A  91 
 PHE   0.016   0.002   PHE A  13 
 TRP   0.010   0.001   TRP A  21 
 HIS   0.006   0.001   HIS A 620 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00254 /  0.14 (14377)
  covalent geometry    : angle       0.53423 /  0.33 (20898)
  hydrogen bonds       : bond        0.04798 /  4.78 (  681)
  hydrogen bonds       : angle       3.33680 /  3.92 ( 1686)
  metal coordination   : bond        0.00610 /  0.41 (    8)
  metal coordination   : angle       2.29392 /  4.29 (    9)

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.297 
Fit side-chains
REVERT: A  336 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7674 (mtt180)
REVERT: A  341 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7670 (mp-120)
REVERT: A  477 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8712 (tp)
REVERT: A  566 LYS cc_start: 0.8206 (tttp) cc_final: 0.7930 (ttmp)
REVERT: B    9 LYS cc_start: 0.7213 (ttpt) cc_final: 0.6520 (ttpt)
REVERT: B   15 ASN cc_start: 0.8043 (OUTLIER) cc_final: 0.7562 (t0)
REVERT: B   89 ARG cc_start: 0.7602 (mtm-85) cc_final: 0.7390 (mtm180)
REVERT: C   93 GLN cc_start: 0.8583 (mt0) cc_final: 0.7215 (pm20)
REVERT: C  161 MET cc_start: 0.8538 (mtm) cc_final: 0.8307 (mtt)
  outliers start: 16
  outliers final: 2
  residues processed: 98
  average time/residue: 0.8800
  time to fit residues: 91.1890
Evaluate side-chains
  97 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 91
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  341 GLN
Chi-restraints excluded: chain A residue  477 ILE
Chi-restraints excluded: chain B residue   15 ASN
Chi-restraints excluded: chain C residue   73 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 47 optimal weight:    8.9990
   chunk 84 optimal weight:    8.9990
   chunk 63 optimal weight:    0.0040
   chunk 18 optimal weight:   20.0000
   chunk 59 optimal weight:    4.9990
   chunk 88 optimal weight:    0.6980
   chunk 29 optimal weight:   10.0000
   chunk 43 optimal weight:    0.9990
   chunk 34 optimal weight:   10.0000
   chunk 87 optimal weight:    0.8980
   chunk 108 optimal weight:   30.0000
   overall best weight:    1.5196

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  49 GLN
A 620 HIS
B  80 GLN
C 137 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.179536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.138974 restraints weight = 12185.227|
|-----------------------------------------------------------------------------|
r_work (start): 0.3567 rms_B_bonded: 0.85
r_work: 0.3333 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3236 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8652
moved from start:          0.2005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.053  14385  Z= 0.128
  Angle     :  0.524   6.827  20907  Z= 0.321
  Chirality :  0.040   0.288   2524
  Planarity :  0.004   0.041   1532
  Dihedral  : 23.930 178.267   5469
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 11.98 %
    Favored  : 86.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.05 (0.29), residues: 843
  helix:  1.97 (0.23), residues: 504
  sheet:  0.66 (0.67), residues: 65
  loop :  0.52 (0.39), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 100 
 TYR   0.015   0.001   TYR A  91 
 PHE   0.016   0.001   PHE A  13 
 TRP   0.010   0.001   TRP A 111 
 HIS   0.005   0.001   HIS A 620 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00219 /  0.13 (14377)
  covalent geometry    : angle       0.52188 /  0.32 (20898)
  hydrogen bonds       : bond        0.04611 /  4.62 (  681)
  hydrogen bonds       : angle       3.29347 /  3.88 ( 1686)
  metal coordination   : bond        0.00445 /  0.30 (    8)
  metal coordination   : angle       2.18650 /  4.11 (    9)

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.356 
Fit side-chains
REVERT: A  336 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7679 (mtt180)
REVERT: A  341 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7646 (mp-120)
REVERT: A  477 ILE cc_start: 0.8961 (OUTLIER) cc_final: 0.8688 (tp)
REVERT: A  566 LYS cc_start: 0.8176 (tttp) cc_final: 0.7892 (ttmp)
REVERT: B    9 LYS cc_start: 0.7229 (ttpt) cc_final: 0.6558 (ttpt)
REVERT: C   93 GLN cc_start: 0.8573 (mt0) cc_final: 0.7233 (pm20)
REVERT: C  161 MET cc_start: 0.8551 (mtm) cc_final: 0.8218 (mtt)
  outliers start: 13
  outliers final: 4
  residues processed: 97
  average time/residue: 0.8878
  time to fit residues: 91.1444
Evaluate side-chains
  100 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 93
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  341 GLN
Chi-restraints excluded: chain A residue  477 ILE
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  123 ASP
Chi-restraints excluded: chain C residue  163 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 106 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 2 optimal weight:   50.0000
   chunk 57 optimal weight:   10.0000
   chunk 24 optimal weight:   20.0000
   chunk 83 optimal weight:    1.9990
   chunk 101 optimal weight:    4.9990
   chunk 103 optimal weight:    7.9990
   chunk 27 optimal weight:   20.0000
   chunk 53 optimal weight:   10.0000
   overall best weight:    4.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 431 ASN
B  80 GLN
C 135 ASN
C 137 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.176708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.134185 restraints weight = 12071.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.3505 rms_B_bonded: 0.82
r_work: 0.3289 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3183 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8707
moved from start:          0.1942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  14385  Z= 0.191
  Angle     :  0.591   7.282  20907  Z= 0.351
  Chirality :  0.044   0.341   2524
  Planarity :  0.005   0.037   1532
  Dihedral  : 23.933 178.580   5469
  Min Nonbonded Distance : 1.906

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 12.65 %
    Favored  : 85.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.90 (0.29), residues: 843
  helix:  1.79 (0.22), residues: 505
  sheet:  0.70 (0.66), residues: 65
  loop :  0.55 (0.40), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 100 
 TYR   0.021   0.002   TYR A  91 
 PHE   0.020   0.002   PHE A  13 
 TRP   0.011   0.002   TRP A 382 
 HIS   0.004   0.001   HIS C  24 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00364 /  0.19 (14377)
  covalent geometry    : angle       0.58865 /  0.35 (20898)
  hydrogen bonds       : bond        0.05273 /  5.28 (  681)
  hydrogen bonds       : angle       3.39855 /  3.99 ( 1686)
  metal coordination   : bond        0.00881 /  0.59 (    8)
  metal coordination   : angle       2.49039 /  4.68 (    9)

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.328 
Fit side-chains
REVERT: A  275 ARG cc_start: 0.7575 (tmm160) cc_final: 0.6946 (tpp80)
REVERT: A  336 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7702 (mtt180)
REVERT: A  341 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7705 (mp-120)
REVERT: A  420 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.7310 (tm-30)
REVERT: A  477 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8747 (tp)
REVERT: A  566 LYS cc_start: 0.8254 (tttp) cc_final: 0.7932 (ttmp)
REVERT: B    9 LYS cc_start: 0.7074 (ttpt) cc_final: 0.6378 (ttpt)
REVERT: C   93 GLN cc_start: 0.8630 (mt0) cc_final: 0.7270 (pm20)
  outliers start: 11
  outliers final: 3
  residues processed: 98
  average time/residue: 0.9974
  time to fit residues: 103.3331
Evaluate side-chains
  102 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  341 GLN
Chi-restraints excluded: chain A residue  420 GLN
Chi-restraints excluded: chain A residue  477 ILE
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  163 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 18 optimal weight:   20.0000
   chunk 14 optimal weight:   20.0000
   chunk 97 optimal weight:    6.9990
   chunk 43 optimal weight:    0.9990
   chunk 89 optimal weight:    5.9990
   chunk 71 optimal weight:    5.9990
   chunk 41 optimal weight:    8.9990
   chunk 93 optimal weight:    2.9990
   chunk 113 optimal weight:    8.9990
   chunk 58 optimal weight:    1.9990
   chunk 103 optimal weight:    5.9990
   overall best weight:    3.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 431 ASN
A 620 HIS
B  80 GLN
C 137 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.177162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.134988 restraints weight = 12121.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.3517 rms_B_bonded: 0.80
r_work: 0.3295 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3192 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8701
moved from start:          0.1988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  14385  Z= 0.173
  Angle     :  0.571   7.748  20907  Z= 0.342
  Chirality :  0.042   0.327   2524
  Planarity :  0.004   0.035   1532
  Dihedral  : 23.950 178.805   5469
  Min Nonbonded Distance : 1.920

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 12.79 %
    Favored  : 85.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.89 (0.29), residues: 843
  helix:  1.80 (0.22), residues: 505
  sheet:  0.67 (0.66), residues: 65
  loop :  0.52 (0.39), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  39 
 TYR   0.018   0.002   TYR A  91 
 PHE   0.019   0.002   PHE A  13 
 TRP   0.011   0.002   TRP A  21 
 HIS   0.004   0.001   HIS A 620 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00324 /  0.17 (14377)
  covalent geometry    : angle       0.56855 /  0.34 (20898)
  hydrogen bonds       : bond        0.05100 /  5.11 (  681)
  hydrogen bonds       : angle       3.39435 /  3.99 ( 1686)
  metal coordination   : bond        0.00885 /  0.59 (    8)
  metal coordination   : angle       2.44955 /  4.61 (    9)

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.375 
Fit side-chains
REVERT: A  275 ARG cc_start: 0.7563 (tmm160) cc_final: 0.6924 (tpp80)
REVERT: A  336 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7697 (mtt180)
REVERT: A  341 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7714 (mp-120)
REVERT: A  420 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.7334 (tm-30)
REVERT: A  477 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8736 (tp)
REVERT: A  566 LYS cc_start: 0.8250 (tttp) cc_final: 0.7931 (ttmp)
REVERT: B    9 LYS cc_start: 0.7067 (ttpt) cc_final: 0.6314 (ttpt)
REVERT: C   93 GLN cc_start: 0.8619 (mt0) cc_final: 0.7260 (pm20)
REVERT: C  121 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7641 (ptpt)
  outliers start: 12
  outliers final: 3
  residues processed: 98
  average time/residue: 1.0127
  time to fit residues: 104.8175
Evaluate side-chains
  100 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  341 GLN
Chi-restraints excluded: chain A residue  420 GLN
Chi-restraints excluded: chain A residue  477 ILE
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  121 LYS
Chi-restraints excluded: chain C residue  163 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 38 optimal weight:    8.9990
   chunk 84 optimal weight:    4.9990
   chunk 57 optimal weight:    9.9990
   chunk 36 optimal weight:    2.9990
   chunk 55 optimal weight:    4.9990
   chunk 7 optimal weight:   20.0000
   chunk 6 optimal weight:   40.0000
   chunk 11 optimal weight:   20.0000
   chunk 46 optimal weight:   20.0000
   chunk 63 optimal weight:    8.9990
   chunk 0 optimal weight:   20.0000
   overall best weight:    6.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 431 ASN
B  80 GLN
C 135 ASN
C 137 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.174774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.132248 restraints weight = 12069.813|
|-----------------------------------------------------------------------------|
r_work (start): 0.3482 rms_B_bonded: 0.93
r_work: 0.3266 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3163 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8728
moved from start:          0.1966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  14385  Z= 0.253
  Angle     :  0.667   8.057  20907  Z= 0.387
  Chirality :  0.048   0.376   2524
  Planarity :  0.005   0.044   1532
  Dihedral  : 23.994 178.985   5469
  Min Nonbonded Distance : 1.872

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 13.59 %
    Favored  : 85.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.62 (0.29), residues: 843
  helix:  1.54 (0.22), residues: 505
  sheet:  0.71 (0.65), residues: 65
  loop :  0.46 (0.39), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  61 
 TYR   0.023   0.003   TYR A  91 
 PHE   0.023   0.003   PHE A  13 
 TRP   0.014   0.002   TRP A 382 
 HIS   0.004   0.001   HIS B  43 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00504 /  0.25 (14377)
  covalent geometry    : angle       0.66491 /  0.39 (20898)
  hydrogen bonds       : bond        0.05892 /  5.89 (  681)
  hydrogen bonds       : angle       3.53422 /  4.13 ( 1686)
  metal coordination   : bond        0.01335 /  0.89 (    8)
  metal coordination   : angle       2.90287 /  5.49 (    9)

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 96
  time to evaluate  : 0.365 
Fit side-chains
REVERT: A  275 ARG cc_start: 0.7624 (tmm160) cc_final: 0.6988 (tpp80)
REVERT: A  336 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7689 (mtt180)
REVERT: A  341 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7705 (mp-120)
REVERT: A  477 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8800 (tp)
REVERT: A  566 LYS cc_start: 0.8320 (tttp) cc_final: 0.7997 (ttmp)
REVERT: B    9 LYS cc_start: 0.7187 (ttpt) cc_final: 0.6425 (ttpt)
REVERT: C   93 GLN cc_start: 0.8642 (mt0) cc_final: 0.7261 (pm20)
REVERT: C  121 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7686 (ptpt)
  outliers start: 6
  outliers final: 2
  residues processed: 98
  average time/residue: 0.9204
  time to fit residues: 95.3183
Evaluate side-chains
  100 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 94
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  341 GLN
Chi-restraints excluded: chain A residue  477 ILE
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  121 LYS
Chi-restraints excluded: chain C residue  163 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 54 optimal weight:    9.9990
   chunk 90 optimal weight:    9.9990
   chunk 4 optimal weight:   30.0000
   chunk 83 optimal weight:    3.9990
   chunk 0 optimal weight:   20.0000
   chunk 79 optimal weight:    6.9990
   chunk 26 optimal weight:   50.0000
   chunk 48 optimal weight:    6.9990
   chunk 67 optimal weight:   20.0000
   chunk 104 optimal weight:    5.9990
   chunk 10 optimal weight:   20.0000
   overall best weight:    6.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 431 ASN
C 135 ASN
C 137 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.174208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.131975 restraints weight = 12117.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.3480 rms_B_bonded: 0.98
r_work: 0.3256 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3159 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8736
moved from start:          0.2013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  14385  Z= 0.266
  Angle     :  0.689   8.663  20907  Z= 0.398
  Chirality :  0.050   0.385   2524
  Planarity :  0.005   0.046   1532
  Dihedral  : 24.057 179.670   5469
  Min Nonbonded Distance : 1.860

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 13.46 %
    Favored  : 85.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.38 (0.28), residues: 843
  helix:  1.36 (0.22), residues: 505
  sheet:  0.38 (0.65), residues: 62
  loop :  0.42 (0.39), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  61 
 TYR   0.023   0.003   TYR A  91 
 PHE   0.024   0.003   PHE A  13 
 TRP   0.014   0.002   TRP A  21 
 HIS   0.004   0.001   HIS C  24 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00530 /  0.27 (14377)
  covalent geometry    : angle       0.68605 /  0.40 (20898)
  hydrogen bonds       : bond        0.06064 /  6.06 (  681)
  hydrogen bonds       : angle       3.59368 /  4.21 ( 1686)
  metal coordination   : bond        0.01558 /  1.04 (    8)
  metal coordination   : angle       3.05833 /  5.78 (    9)

===============================================================================
Job complete
usr+sys time: 5338.04 seconds
wall clock time: 91 minutes 25.48 seconds (5485.48 seconds total)