Starting phenix.real_space_refine
on Thu Aug  6 04:15:58 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rkt_19282/08_2026/8rkt_19282.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rkt_19282/08_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_19282/08_2026/8rkt_19282.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rkt_19282/08_2026/8rkt_19282.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rkt_19282/08_2026/8rkt_19282.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rkt_19282/08_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-2.2rc3-6140/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: 3.08, per 1000 atoms: 0.22
  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: 1.12
  Conformation dependent library (CDL) restraints added in 386.4 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: 2.11
  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: 3.44

  Time building geometry restraints manager: 1.54 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 -     2.19: 19493
        2.19 -     4.38: 1315
        4.38 -     6.56: 81
        6.56 -     8.75: 8
        8.75 -    10.94: 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
     119.70  108.76   10.94 1.20e+00 6.94e-01 8.31e+01
  angle pdb=" O5'   U 1 100 "
        pdb=" C5'   U 1 100 "
        pdb=" C4'   U 1 100 "
      ideal   model   delta    sigma   weight residual
     109.40  115.65   -6.25 8.00e-01 1.56e+00 6.11e+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=" O5'   U 1  46 "
        pdb=" C5'   U 1  46 "
        pdb=" C4'   U 1  46 "
      ideal   model   delta    sigma   weight residual
     109.40  115.00   -5.60 8.00e-01 1.56e+00 4.90e+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: 2191
       0.124 -    0.249: 308
       0.249 -    0.373: 20
       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:                  0.000
  Normalize map: mean=0, sd=1:             2.050
  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:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     17.440
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  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:             0.010
  Load rotamer database and sin/cos tables:6.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.350
-------------------------------------------------------------------------------
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= 0.511
  Angle     :  1.059  10.940  20907  Z= 0.886
  Chirality :  0.084   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        0.00610 /  0.51 (14377)
  covalent geometry    : angle       1.05837 /  0.89 (20898)
  hydrogen bonds       : bond        0.13813 / 14.92 (  681)
  hydrogen bonds       : angle       5.42584 /  6.52 ( 1686)
  metal coordination   : bond        0.02466 /  2.39 (    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  : 0.470 
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: 0.7809 (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: 0.7380 (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: 0.7399 (tp-100)
REVERT: A  496 GLN cc_start: 0.8474 (mt0) cc_final: 0.8252 (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   61 ARG cc_start: 0.7733 (mtm-85) cc_final: 0.7483 (mtp-110)
REVERT: C   93 GLN cc_start: 0.8254 (mt0) cc_final: 0.7207 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 1.0337
  time to fit residues: 138.0911
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  : 0.357 
-------------------------------------------------------------------------------
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  47 ASN
B  80 GLN
C 135 ASN
C 137 GLN
C 165 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.178103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.137290 restraints weight = 12321.035|
|-----------------------------------------------------------------------------|
r_work (start): 0.3544 rms_B_bonded: 0.82
r_work: 0.3321 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3222 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8682
moved from start:          0.1176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  14385  Z= 0.175
  Angle     :  0.660   9.524  20907  Z= 0.390
  Chirality :  0.048   0.612   2524
  Planarity :  0.005   0.031   1532
  Dihedral  : 23.872 178.928   5469
  Min Nonbonded Distance : 1.947

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  :  6.73 %
    Favored  : 92.06 %
  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:  1.48 (0.29), residues: 843
  helix:  1.29 (0.22), residues: 504
  sheet:  0.81 (0.66), residues: 65
  loop :  0.68 (0.40), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 350 
 TYR   0.024   0.002   TYR A  91 
 PHE   0.021   0.002   PHE A 214 
 TRP   0.013   0.002   TRP A  21 
 HIS   0.006   0.001   HIS C  24 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00320 /  0.18 (14377)
  covalent geometry    : angle       0.65789 /  0.39 (20898)
  hydrogen bonds       : bond        0.06039 /  6.67 (  681)
  hydrogen bonds       : angle       3.72797 /  4.53 ( 1686)
  metal coordination   : bond        0.01346 /  1.24 (    8)
  metal coordination   : angle       2.43298 /  4.40 (    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
  110 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 101
  time to evaluate  : 0.247 
Fit side-chains
REVERT: A  252 LEU cc_start: 0.8723 (mt) cc_final: 0.8503 (mp)
REVERT: A  341 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.7594 (mp-120)
REVERT: A  492 ARG cc_start: 0.8302 (ttp-110) cc_final: 0.7638 (ttp80)
REVERT: B    9 LYS cc_start: 0.7192 (ttpt) cc_final: 0.6703 (ttpt)
  outliers start: 9
  outliers final: 4
  residues processed: 102
  average time/residue: 0.8474
  time to fit residues: 91.7128
Evaluate side-chains
  94 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 89
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain C residue   92 MET
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:    8.9990
   chunk 82 optimal weight:    6.9990
   chunk 92 optimal weight:    3.9990
   chunk 51 optimal weight:    4.9990
   chunk 28 optimal weight:   10.0000
   chunk 52 optimal weight:    8.9990
   chunk 91 optimal weight:    1.9990
   chunk 78 optimal weight:    5.9990
   chunk 47 optimal weight:    0.0370
   chunk 18 optimal weight:   30.0000
   overall best weight:    3.2066

-------------------------------------------------------------------------------
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 = 0.3995 r_free = 0.3995 target = 0.177808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.135689 restraints weight = 12265.768|
|-----------------------------------------------------------------------------|
r_work (start): 0.3528 rms_B_bonded: 0.79
r_work: 0.3302 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3201 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8692
moved from start:          0.1559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  14385  Z= 0.168
  Angle     :  0.606   8.749  20907  Z= 0.357
  Chirality :  0.045   0.581   2524
  Planarity :  0.004   0.034   1532
  Dihedral  : 23.808 178.142   5469
  Min Nonbonded Distance : 1.947

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  :  8.21 %
    Favored  : 90.31 %
  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:  1.82 (0.29), residues: 843
  helix:  1.65 (0.23), residues: 504
  sheet:  0.75 (0.66), residues: 65
  loop :  0.67 (0.40), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 240 
 TYR   0.019   0.002   TYR A  91 
 PHE   0.022   0.002   PHE A  13 
 TRP   0.011   0.002   TRP A 382 
 HIS   0.008   0.001   HIS A 353 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00308 /  0.17 (14377)
  covalent geometry    : angle       0.60436 /  0.36 (20898)
  hydrogen bonds       : bond        0.05458 /  5.98 (  681)
  hydrogen bonds       : angle       3.49007 /  4.28 ( 1686)
  metal coordination   : bond        0.00963 /  0.85 (    8)
  metal coordination   : angle       2.20868 /  4.05 (    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
  105 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 0.362 
Fit side-chains
REVERT: A  252 LEU cc_start: 0.8706 (mt) cc_final: 0.8453 (mp)
REVERT: A  341 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7644 (mp-120)
REVERT: B    9 LYS cc_start: 0.7152 (ttpt) cc_final: 0.6650 (ttpt)
REVERT: C  161 MET cc_start: 0.8593 (mtm) cc_final: 0.8324 (mtt)
  outliers start: 11
  outliers final: 5
  residues processed: 97
  average time/residue: 0.9242
  time to fit residues: 94.8976
Evaluate side-chains
  96 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 90
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
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  420 GLN
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue   92 MET
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:    7.9990
   chunk 67 optimal weight:   10.0000
   chunk 23 optimal weight:   10.0000
   chunk 44 optimal weight:   20.0000
   chunk 76 optimal weight:   10.0000
   chunk 24 optimal weight:   20.0000
   chunk 4 optimal weight:   40.0000
   chunk 74 optimal weight:    4.9990
   chunk 19 optimal weight:   30.0000
   overall best weight:    7.9994

-------------------------------------------------------------------------------
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 620 HIS
B  80 GLN
C 135 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.173865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.131005 restraints weight = 12155.587|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 0.79
r_work: 0.3248 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3144 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8745
moved from start:          0.1688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054  14385  Z= 0.302
  Angle     :  0.791  11.511  20907  Z= 0.435
  Chirality :  0.056   0.706   2524
  Planarity :  0.006   0.055   1532
  Dihedral  : 23.986 179.412   5469
  Min Nonbonded Distance : 1.864

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 10.09 %
    Favored  : 88.16 %
  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:  1.30 (0.28), residues: 843
  helix:  1.21 (0.22), residues: 503
  sheet:  0.31 (0.65), residues: 62
  loop :  0.60 (0.39), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 492 
 TYR   0.028   0.003   TYR A  91 
 PHE   0.028   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        0.00603 /  0.30 (14377)
  covalent geometry    : angle       0.78866 /  0.43 (20898)
  hydrogen bonds       : bond        0.06676 /  7.27 (  681)
  hydrogen bonds       : angle       3.69465 /  4.52 ( 1686)
  metal coordination   : bond        0.01895 /  1.70 (    8)
  metal coordination   : angle       3.00786 /  5.53 (    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
  104 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 0.380 
Fit side-chains
REVERT: A  275 ARG cc_start: 0.7613 (tmm160) cc_final: 0.6991 (tpp80)
REVERT: A  341 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7707 (mp-120)
REVERT: B    9 LYS cc_start: 0.7238 (ttpt) cc_final: 0.6538 (ttpt)
  outliers start: 13
  outliers final: 5
  residues processed: 95
  average time/residue: 0.8635
  time to fit residues: 86.8493
Evaluate side-chains
  95 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 89
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
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 C residue   73 VAL
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:    1.9990
   chunk 36 optimal weight:    6.9990
   chunk 9 optimal weight:   20.0000
   chunk 20 optimal weight:   50.0000
   chunk 58 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 98 optimal weight:   20.0000
   chunk 32 optimal weight:    0.7980
   chunk 27 optimal weight:   20.0000
   chunk 88 optimal weight:    5.9990
   overall best weight:    2.9588

-------------------------------------------------------------------------------
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 = 0.3991 r_free = 0.3991 target = 0.177447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.134729 restraints weight = 12217.028|
|-----------------------------------------------------------------------------|
r_work (start): 0.3515 rms_B_bonded: 0.76
r_work: 0.3310 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3212 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8681
moved from start:          0.1816

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= 0.160
  Angle     :  0.592   8.958  20907  Z= 0.348
  Chirality :  0.044   0.570   2524
  Planarity :  0.004   0.035   1532
  Dihedral  : 23.912 178.646   5469
  Min Nonbonded Distance : 1.949

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  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:  1.67 (0.29), residues: 843
  helix:  1.59 (0.23), residues: 504
  sheet:  0.64 (0.66), residues: 65
  loop :  0.50 (0.39), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 275 
 TYR   0.015   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        0.00289 /  0.16 (14377)
  covalent geometry    : angle       0.59020 /  0.35 (20898)
  hydrogen bonds       : bond        0.05285 /  5.76 (  681)
  hydrogen bonds       : angle       3.47033 /  4.26 ( 1686)
  metal coordination   : bond        0.00913 /  0.78 (    8)
  metal coordination   : angle       2.37312 /  4.41 (    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
  104 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 0.391 
Fit side-chains
REVERT: A  230 GLU cc_start: 0.8282 (mt-10) cc_final: 0.8027 (mt-10)
REVERT: A  336 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7676 (mtt180)
REVERT: A  341 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7669 (mp-120)
REVERT: A  477 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8746 (tp)
REVERT: B    9 LYS cc_start: 0.7265 (ttpt) cc_final: 0.6617 (ttpt)
  outliers start: 13
  outliers final: 3
  residues processed: 95
  average time/residue: 1.0597
  time to fit residues: 106.4727
Evaluate side-chains
  96 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 90
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
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 A residue  477 ILE
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:    3.9990
   chunk 27 optimal weight:   30.0000
   chunk 71 optimal weight:    5.9990
   chunk 46 optimal weight:    6.9990
   chunk 93 optimal weight:    3.9990
   chunk 62 optimal weight:   20.0000
   chunk 83 optimal weight:    5.9990
   chunk 106 optimal weight:    8.9990
   chunk 36 optimal weight:    3.9990
   chunk 63 optimal weight:    0.7980
   chunk 75 optimal weight:    3.9990
   overall best weight:    3.3588

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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.177201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.134715 restraints weight = 12102.335|
|-----------------------------------------------------------------------------|
r_work (start): 0.3515 rms_B_bonded: 0.75
r_work: 0.3302 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3206 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8687
moved from start:          0.1922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  14385  Z= 0.168
  Angle     :  0.597   9.204  20907  Z= 0.348
  Chirality :  0.044   0.584   2524
  Planarity :  0.004   0.034   1532
  Dihedral  : 23.879 179.401   5469
  Min Nonbonded Distance : 1.920

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 10.90 %
    Favored  : 86.54 %
  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:  1.79 (0.29), residues: 843
  helix:  1.67 (0.23), residues: 506
  sheet:  0.67 (0.67), residues: 65
  loop :  0.57 (0.40), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 490 
 TYR   0.019   0.002   TYR A  91 
 PHE   0.019   0.002   PHE A  13 
 TRP   0.011   0.002   TRP A  21 
 HIS   0.005   0.001   HIS A 620 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00312 /  0.17 (14377)
  covalent geometry    : angle       0.59537 /  0.35 (20898)
  hydrogen bonds       : bond        0.05248 /  5.73 (  681)
  hydrogen bonds       : angle       3.41937 /  4.19 ( 1686)
  metal coordination   : bond        0.00831 /  0.68 (    8)
  metal coordination   : angle       2.45352 /  4.59 (    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
  112 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 93
  time to evaluate  : 0.379 
Fit side-chains
REVERT: A  230 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8084 (mt-10)
REVERT: A  275 ARG cc_start: 0.7572 (tmm160) cc_final: 0.6884 (tpt170)
REVERT: A  336 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7672 (mtt180)
REVERT: A  341 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7670 (mp-120)
REVERT: A  477 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8750 (tp)
REVERT: B    9 LYS cc_start: 0.7256 (ttpt) cc_final: 0.6577 (ttpt)
REVERT: C  161 MET cc_start: 0.8547 (mtm) cc_final: 0.8242 (mtt)
  outliers start: 19
  outliers final: 4
  residues processed: 100
  average time/residue: 0.9536
  time to fit residues: 100.9856
Evaluate side-chains
  101 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 94
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 PHE
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 A residue  477 ILE
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:    0.9990
   chunk 84 optimal weight:    5.9990
   chunk 63 optimal weight:    0.9990
   chunk 18 optimal weight:   30.0000
   chunk 59 optimal weight:    8.9990
   chunk 88 optimal weight:    1.9990
   chunk 29 optimal weight:   10.0000
   chunk 43 optimal weight:    3.9990
   chunk 34 optimal weight:   10.0000
   chunk 87 optimal weight:   10.0000
   chunk 108 optimal weight:    6.9990
   overall best weight:    2.7990

-------------------------------------------------------------------------------
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 = 0.3995 r_free = 0.3995 target = 0.177881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.135489 restraints weight = 12091.043|
|-----------------------------------------------------------------------------|
r_work (start): 0.3528 rms_B_bonded: 0.75
r_work: 0.3316 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3215 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8677
moved from start:          0.1970

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= 0.152
  Angle     :  0.572   8.786  20907  Z= 0.337
  Chirality :  0.043   0.562   2524
  Planarity :  0.004   0.037   1532
  Dihedral  : 23.872 179.178   5469
  Min Nonbonded Distance : 1.942

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 11.57 %
    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:  1.87 (0.29), residues: 843
  helix:  1.77 (0.23), residues: 505
  sheet:  0.62 (0.67), residues: 65
  loop :  0.57 (0.39), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  89 
 TYR   0.016   0.002   TYR A  91 
 PHE   0.018   0.002   PHE A  13 
 TRP   0.011   0.001   TRP A  21 
 HIS   0.004   0.001   HIS A 620 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00273 /  0.15 (14377)
  covalent geometry    : angle       0.57043 /  0.34 (20898)
  hydrogen bonds       : bond        0.05042 /  5.52 (  681)
  hydrogen bonds       : angle       3.37988 /  4.14 ( 1686)
  metal coordination   : bond        0.00732 /  0.60 (    8)
  metal coordination   : angle       2.39181 /  4.46 (    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
  107 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.375 
Fit side-chains
REVERT: A  230 GLU cc_start: 0.8320 (mt-10) cc_final: 0.8096 (mt-10)
REVERT: A  275 ARG cc_start: 0.7551 (tmm160) cc_final: 0.6919 (tpp80)
REVERT: A  336 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7668 (mtt180)
REVERT: A  341 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7670 (mp-120)
REVERT: A  477 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8723 (tp)
REVERT: B    9 LYS cc_start: 0.7171 (ttpt) cc_final: 0.6430 (ttpt)
REVERT: B   15 ASN cc_start: 0.8027 (OUTLIER) cc_final: 0.7611 (t0)
REVERT: B   76 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.7358 (mtt90)
  outliers start: 15
  outliers final: 6
  residues processed: 98
  average time/residue: 0.9840
  time to fit residues: 101.9783
Evaluate side-chains
  100 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 89
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue  216 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 A residue  477 ILE
Chi-restraints excluded: chain B residue   15 ASN
Chi-restraints excluded: chain B residue   76 ARG
Chi-restraints excluded: chain C residue   73 VAL
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:   30.0000
   chunk 106 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 2 optimal weight:   50.0000
   chunk 57 optimal weight:    9.9990
   chunk 24 optimal weight:   20.0000
   chunk 83 optimal weight:   10.0000
   chunk 101 optimal weight:    4.9990
   chunk 103 optimal weight:    6.9990
   chunk 27 optimal weight:   20.0000
   chunk 53 optimal weight:    8.9990
   overall best weight:    5.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.175684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.133111 restraints weight = 12029.806|
|-----------------------------------------------------------------------------|
r_work (start): 0.3492 rms_B_bonded: 0.75
r_work: 0.3278 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3175 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8714
moved from start:          0.1961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  14385  Z= 0.214
  Angle     :  0.657  10.114  20907  Z= 0.373
  Chirality :  0.048   0.630   2524
  Planarity :  0.005   0.036   1532
  Dihedral  : 23.916 179.875   5469
  Min Nonbonded Distance : 1.884

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 11.57 %
    Favored  : 86.54 %
  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:  1.67 (0.29), residues: 843
  helix:  1.56 (0.22), residues: 506
  sheet:  0.68 (0.65), residues: 65
  loop :  0.54 (0.40), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 490 
 TYR   0.023   0.002   TYR A  91 
 PHE   0.022   0.002   PHE A  13 
 TRP   0.013   0.002   TRP A 382 
 HIS   0.006   0.001   HIS A 620 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00416 /  0.21 (14377)
  covalent geometry    : angle       0.65476 /  0.37 (20898)
  hydrogen bonds       : bond        0.05685 /  6.21 (  681)
  hydrogen bonds       : angle       3.49427 /  4.28 ( 1686)
  metal coordination   : bond        0.01047 /  0.87 (    8)
  metal coordination   : angle       2.66974 /  5.04 (    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: 14
    poor density    : 93
  time to evaluate  : 0.370 
Fit side-chains
REVERT: A  230 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8112 (mt-10)
REVERT: A  275 ARG cc_start: 0.7605 (tmm160) cc_final: 0.6952 (tpp80)
REVERT: A  336 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7694 (mtt180)
REVERT: A  341 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7682 (mp-120)
REVERT: A  420 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.7251 (tm-30)
REVERT: A  477 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8769 (tp)
REVERT: B    9 LYS cc_start: 0.7181 (ttpt) cc_final: 0.6410 (ttpt)
REVERT: B   76 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7393 (mtt90)
REVERT: C  161 MET cc_start: 0.8590 (mtm) cc_final: 0.8210 (mtt)
  outliers start: 14
  outliers final: 5
  residues processed: 96
  average time/residue: 0.9477
  time to fit residues: 96.4255
Evaluate side-chains
  102 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 92
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
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  339 LYS
Chi-restraints excluded: chain A residue  341 GLN
Chi-restraints excluded: chain A residue  420 GLN
Chi-restraints excluded: chain A residue  438 GLN
Chi-restraints excluded: chain A residue  477 ILE
Chi-restraints excluded: chain B residue   76 ARG
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:   30.0000
   chunk 14 optimal weight:   20.0000
   chunk 97 optimal weight:    5.9990
   chunk 43 optimal weight:    6.9990
   chunk 89 optimal weight:    9.9990
   chunk 71 optimal weight:    7.9990
   chunk 41 optimal weight:    5.9990
   chunk 93 optimal weight:    1.9990
   chunk 113 optimal weight:    4.9990
   chunk 58 optimal weight:    4.9990
   chunk 103 optimal weight:    2.9990
   overall best weight:    4.1990

-------------------------------------------------------------------------------
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 = 0.3982 r_free = 0.3982 target = 0.176560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.134237 restraints weight = 12096.530|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 0.78
r_work: 0.3287 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3185 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8709
moved from start:          0.2014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  14385  Z= 0.186
  Angle     :  0.618   9.434  20907  Z= 0.356
  Chirality :  0.045   0.598   2524
  Planarity :  0.004   0.035   1532
  Dihedral  : 23.912 179.935   5469
  Min Nonbonded Distance : 1.907

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.83 %
    Favored  : 99.17 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 11.84 %
    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:  1.73 (0.29), residues: 843
  helix:  1.62 (0.22), residues: 506
  sheet:  0.71 (0.66), residues: 65
  loop :  0.52 (0.39), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 490 
 TYR   0.019   0.002   TYR A  91 
 PHE   0.020   0.002   PHE A  13 
 TRP   0.012   0.002   TRP A  21 
 HIS   0.004   0.001   HIS A 620 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00355 /  0.19 (14377)
  covalent geometry    : angle       0.61584 /  0.36 (20898)
  hydrogen bonds       : bond        0.05372 /  5.88 (  681)
  hydrogen bonds       : angle       3.45086 /  4.22 ( 1686)
  metal coordination   : bond        0.00990 /  0.85 (    8)
  metal coordination   : angle       2.57309 /  4.83 (    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
  103 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.398 
Fit side-chains
REVERT: A  230 GLU cc_start: 0.8298 (mt-10) cc_final: 0.8069 (mt-10)
REVERT: A  275 ARG cc_start: 0.7606 (tmm160) cc_final: 0.6959 (tpp80)
REVERT: A  336 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7688 (mtt180)
REVERT: A  341 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7698 (mp-120)
REVERT: A  420 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.7254 (tm-30)
REVERT: A  477 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8750 (tp)
REVERT: B    9 LYS cc_start: 0.7219 (ttpt) cc_final: 0.6445 (ttpt)
REVERT: B   76 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7378 (mtt90)
  outliers start: 13
  outliers final: 5
  residues processed: 94
  average time/residue: 1.0559
  time to fit residues: 104.8774
Evaluate side-chains
  100 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 90
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 PHE
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  420 GLN
Chi-restraints excluded: chain A residue  438 GLN
Chi-restraints excluded: chain A residue  477 ILE
Chi-restraints excluded: chain B residue   76 ARG
Chi-restraints excluded: chain C residue   73 VAL
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:    7.9990
   chunk 84 optimal weight:    2.9990
   chunk 57 optimal weight:   10.0000
   chunk 36 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   chunk 7 optimal weight:   30.0000
   chunk 6 optimal weight:   40.0000
   chunk 11 optimal weight:   30.0000
   chunk 46 optimal weight:   20.0000
   chunk 63 optimal weight:    5.9990
   chunk 0 optimal weight:   30.0000
   overall best weight:    4.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  49 GLN
A 431 ASN
A 620 HIS
B  80 GLN
C 137 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.175783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.133462 restraints weight = 12045.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.3501 rms_B_bonded: 0.75
r_work: 0.3287 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3186 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8709
moved from start:          0.2053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  14385  Z= 0.205
  Angle     :  0.646   9.926  20907  Z= 0.368
  Chirality :  0.047   0.623   2524
  Planarity :  0.005   0.035   1532
  Dihedral  : 23.932 179.560   5469
  Min Nonbonded Distance : 1.889

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 12.52 %
    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:  1.64 (0.29), residues: 843
  helix:  1.55 (0.22), residues: 506
  sheet:  0.68 (0.66), residues: 65
  loop :  0.49 (0.39), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 490 
 TYR   0.021   0.002   TYR A  91 
 PHE   0.021   0.002   PHE A  13 
 TRP   0.013   0.002   TRP A 382 
 HIS   0.005   0.001   HIS A 620 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00398 /  0.20 (14377)
  covalent geometry    : angle       0.64407 /  0.37 (20898)
  hydrogen bonds       : bond        0.05562 /  6.09 (  681)
  hydrogen bonds       : angle       3.48946 /  4.27 ( 1686)
  metal coordination   : bond        0.01062 /  0.90 (    8)
  metal coordination   : angle       2.73474 /  5.15 (    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
  103 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 0.327 
Fit side-chains
REVERT: A  230 GLU cc_start: 0.8286 (mt-10) cc_final: 0.8051 (mt-10)
REVERT: A  275 ARG cc_start: 0.7614 (tmm160) cc_final: 0.6963 (tpp80)
REVERT: A  336 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7684 (mtt180)
REVERT: A  341 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7694 (mp-120)
REVERT: A  420 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.7259 (tm-30)
REVERT: A  477 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8760 (tp)
REVERT: B    9 LYS cc_start: 0.7159 (ttpt) cc_final: 0.6383 (ttpt)
REVERT: B   76 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7391 (mtt90)
  outliers start: 12
  outliers final: 4
  residues processed: 94
  average time/residue: 1.0638
  time to fit residues: 105.8039
Evaluate side-chains
  101 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 PHE
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  420 GLN
Chi-restraints excluded: chain A residue  477 ILE
Chi-restraints excluded: chain B residue   76 ARG
Chi-restraints excluded: chain C residue   73 VAL
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:   10.0000
   chunk 90 optimal weight:    6.9990
   chunk 4 optimal weight:   40.0000
   chunk 83 optimal weight:    0.7980
   chunk 0 optimal weight:   30.0000
   chunk 79 optimal weight:    6.9990
   chunk 26 optimal weight:   50.0000
   chunk 48 optimal weight:    5.9990
   chunk 67 optimal weight:   20.0000
   chunk 104 optimal weight:   20.0000
   chunk 10 optimal weight:   20.0000
   overall best weight:    6.1590

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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.174676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.132178 restraints weight = 12096.988|
|-----------------------------------------------------------------------------|
r_work (start): 0.3481 rms_B_bonded: 0.79
r_work: 0.3261 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3159 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8735
moved from start:          0.2060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  14385  Z= 0.243
  Angle     :  0.702  10.496  20907  Z= 0.392
  Chirality :  0.050   0.648   2524
  Planarity :  0.005   0.041   1532
  Dihedral  : 23.993 178.825   5469
  Min Nonbonded Distance : 1.865

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 13.06 %
    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:  1.46 (0.28), residues: 843
  helix:  1.40 (0.22), residues: 506
  sheet:  0.74 (0.66), residues: 63
  loop :  0.41 (0.39), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 240 
 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   0.006   0.002   HIS C  24 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00482 /  0.24 (14377)
  covalent geometry    : angle       0.69901 /  0.39 (20898)
  hydrogen bonds       : bond        0.05973 /  6.55 (  681)
  hydrogen bonds       : angle       3.55706 /  4.36 ( 1686)
  metal coordination   : bond        0.01197 /  1.00 (    8)
  metal coordination   : angle       2.98039 /  5.63 (    9)

===============================================================================
Job complete
usr+sys time: 5689.73 seconds
wall clock time: 97 minutes 29.23 seconds (5849.23 seconds total)