Starting phenix.real_space_refine
on Tue Aug  4 17:40:39 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9yro_73372/08_2026/9yro_73372.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9yro_73372/08_2026/9yro_73372.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.55
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9yro_73372/08_2026/9yro_73372.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9yro_73372/08_2026/9yro_73372.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9yro_73372/08_2026/9yro_73372.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9yro_73372/08_2026/9yro_73372.cif"
  }
  resolution = 2.55
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.017
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: 8
    Type Number    sf(0)   Gaussians
     Zn      5      6.06       5
     P      17      5.49       5
     Mg      1      5.21       5
     S      52      5.16       5
     C    3396      2.51       5
     N     926      2.21       5
     O    1040      1.98       5
     F       1      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  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: 5438
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 131, 955
          Classifications: {'peptide': 131}
          Link IDs: {'PTRANS': 7, 'TRANS': 123}
    Chain: "B"
      Number of atoms: 4117
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 510, 4067
          Classifications: {'peptide': 510}
          Link IDs: {'PTRANS': 26, 'TRANS': 483}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 510, 4067
          Classifications: {'peptide': 510}
          Link IDs: {'PTRANS': 26, 'TRANS': 483}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 4131
    Chain: "E"
      Number of atoms: 339
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 339
          Classifications: {'RNA': 16}
          Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 8}
          Link IDs: {'rna3p': 15}
          Chain breaks: 1
    Chain: "A"
      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: "B"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {' MG': 1, ' ZN': 3}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "E"
      Number of atoms: 21
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 21
          Unusual residues: {'K5X': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    520  SG  CYS A  74      31.535  27.487  31.403  1.00 54.87           S
  ATOM    546  SG  CYS A  77      34.694  29.392  30.393  1.00 56.91           S
  ATOM    651  SG  CYS A  90      34.109  25.909  29.020  1.00 61.29           S
  ATOM    854  SG  CYS A 117      22.610  11.403  22.049  1.00 72.92           S
  ATOM    874  SG  CYS A 120      21.975  13.002  18.755  1.00 76.31           S
  ATOM    935  SG  CYS A 128      19.150  12.600  21.300  1.00 83.31           S
  ATOM    947  SG  CYS A 130      20.258   9.610  19.437  1.00 96.56           S
  ATOM   2577  SG  CYS B 207      29.969  21.412  62.857  1.00 53.43           S
  ATOM   2597  SG  CYS B 210      28.460  21.747  66.312  1.00 57.59           S
  ATOM   2718  SG  CYS B 226      31.058  24.284  65.229  1.00 54.56           S
  ATOM   3018  SG  CYS B 261      41.329  55.350  70.447  1.00 53.43           S
  ATOM   3198  SG  CYS B 279      38.387  53.111  69.047  1.00 59.53           S
  ATOM   4588  SG  CYS B 452      23.629  33.009 116.187  1.00 98.44           S
  ATOM   4684  SG  CYS B 477      27.147  33.694 114.926  1.00 74.81           S
  ATOM   4726  SG  CYS B 484      24.851  31.184 113.135  1.00 87.05           S

  Residues with excluded nonbonded symmetry interactions: 7
    residue:
      pdb=" N  AHIS B 264 " occ=0.52
      ... (18 atoms not shown)
      pdb=" NE2BHIS B 264 " occ=0.48
    residue:
      pdb=" N  AGLY B 265 " occ=0.52
      ... (6 atoms not shown)
      pdb=" O  BGLY B 265 " occ=0.48
    residue:
      pdb=" N  AASN B 266 " occ=0.52
      ... (14 atoms not shown)
      pdb=" ND2BASN B 266 " occ=0.48
    residue:
      pdb=" N  AALA B 267 " occ=0.52
      ... (8 atoms not shown)
      pdb=" CB BALA B 267 " occ=0.48
    residue:
      pdb=" N  AHIS B 268 " occ=0.52
      ... (18 atoms not shown)
      pdb=" NE2BHIS B 268 " occ=0.48
    residue:
      pdb=" N  AVAL B 269 " occ=0.52
      ... (12 atoms not shown)
      pdb=" CG2BVAL B 269 " occ=0.48
    residue:
      pdb=" N  AALA B 270 " occ=0.52
      ... (8 atoms not shown)
      pdb=" CB BALA B 270 " occ=0.48
  Time building chain proxies: 1.94, per 1000 atoms: 0.36
  Number of scatterers: 5438
  At special positions: 0
  Unit cell: (68.4796, 83.286, 129.556, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 8
    Type Number    sf(0)
     Zn      5     29.99
     S      52     16.00
     P      17     15.00
     Mg      1     11.99
     F       1      9.00
     O    1040      8.00
     N     926      7.00
     C    3396      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.40
  Conformation dependent library (CDL) restraints added in 359.2 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 201 "
        pdb="ZN    ZN A 201 " - pdb=" NE2 HIS A  83 "
        pdb="ZN    ZN A 201 " - pdb=" SG  CYS A  90 "
        pdb="ZN    ZN A 201 " - pdb=" SG  CYS A  77 "
        pdb="ZN    ZN A 201 " - pdb=" SG  CYS A  74 "
      pdb="  ZN A 202 "
        pdb="ZN    ZN A 202 " - pdb=" SG  CYS A 128 "
        pdb="ZN    ZN A 202 " - pdb=" SG  CYS A 117 "
        pdb="ZN    ZN A 202 " - pdb=" SG  CYS A 120 "
        pdb="ZN    ZN A 202 " - pdb=" SG  CYS A 130 "
      pdb="  ZN B 602 "
        pdb="ZN    ZN B 602 " - pdb=" ND1 HIS B 229 "
        pdb="ZN    ZN B 602 " - pdb=" SG  CYS B 210 "
        pdb="ZN    ZN B 602 " - pdb=" SG  CYS B 226 "
        pdb="ZN    ZN B 602 " - pdb=" SG  CYS B 207 "
      pdb="  ZN B 604 "
        pdb="ZN    ZN B 604 " - pdb=" ND1 HIS B 487 "
        pdb="ZN    ZN B 604 " - pdb=" SG  CYS B 452 "
        pdb="ZN    ZN B 604 " - pdb=" SG  CYS B 477 "
        pdb="ZN    ZN B 604 " - pdb=" SG  CYS B 484 "
      Number of angles added : 15


  1288 Ramachandran restraints generated.
    644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1212

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 9 sheets defined
      29.8% alpha, 16.8% beta
      8 base pairs and 13 stacking pairs defined.
    Time for finding SS restraints: 0.52
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 11
    Processing helix  chain 'A' and resid 12 through 20
      removed outlier: 3.817A  pdb=" N   PHE A  19 " --> pdb=" O   SER A  15 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 22 through 33
    Processing helix  chain 'A' and resid 71 through 73
      No H-bonds generated for 'chain 'A' and resid 71 through 73'
    Processing helix  chain 'A' and resid 74 through 80
    Processing helix  chain 'A' and resid 106 through 114
    Processing helix  chain 'B' and resid 75 through 82
      removed outlier: 3.645A  pdb=" N   ARG B  81 " --> pdb=" O   GLU B  77 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 155
      removed outlier: 3.971A  pdb=" N   LYS B 147 " --> pdb=" O   ASP B 144 " (cutoff:3.500A)
      removed outlier: 5.234A  pdb=" N   HIS B 148 " --> pdb=" O   GLN B 145 " (cutoff:3.500A)
      Proline residue:  B 151  - end of helix
      removed outlier: 3.598A  pdb=" N   LYS B 155 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 175
      removed outlier: 3.967A  pdb=" N   ILE B 164 " --> pdb=" O   ASN B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 196
      removed outlier: 4.085A  pdb=" N   ALA B 191 " --> pdb=" O   ALA B 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 245 through 248
      removed outlier: 3.660A  pdb=" N   GLY B 248 " --> pdb=" O   GLN B 245 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 245 through 248'
    Processing helix  chain 'B' and resid 252 through 258
    Processing helix  chain 'B' and resid 269 through 287
      removed outlier: 3.564A  pdb=" N   ASP B 273 " --> pdb=" O  AVAL B 269 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   VAL B 287 " --> pdb=" O   HIS B 283 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 301 through 325
    Processing helix  chain 'B' and resid 432 through 437
      removed outlier: 3.788A  pdb=" N   VAL B 437 " --> pdb=" O   SER B 434 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 475 through 480
      removed outlier: 3.593A  pdb=" N   LEU B 479 " --> pdb=" O   THR B 475 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   GLY B 480 " --> pdb=" O   ARG B 476 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 475 through 480'
    Processing helix  chain 'B' and resid 484 through 505
      removed outlier: 3.535A  pdb=" N   ALA B 497 " --> pdb=" O   LEU B 493 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 515 through 522
      removed outlier: 4.012A  pdb=" N   LEU B 519 " --> pdb=" O   ASP B 515 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 56
    Processing sheet with id=AA2, first strand: chain 'B' and resid 34 through 35
    Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 55
      removed outlier: 4.624A  pdb=" N   TYR B 124 " --> pdb=" O   ILE B  55 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 116 through 118
      removed outlier: 6.643A  pdb=" N   GLU B  92 " --> pdb=" O   LEU B 107 " (cutoff:3.500A)
      removed outlier: 4.619A  pdb=" N   LEU B 109 " --> pdb=" O   ASP B  90 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   ASP B  90 " --> pdb=" O   LEU B 109 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   PHE B 111 " --> pdb=" O   GLY B  88 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   GLY B  88 " --> pdb=" O   PHE B 111 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 116 through 118
      removed outlier: 6.643A  pdb=" N   GLU B  92 " --> pdb=" O   LEU B 107 " (cutoff:3.500A)
      removed outlier: 4.619A  pdb=" N   LEU B 109 " --> pdb=" O   ASP B  90 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   ASP B  90 " --> pdb=" O   LEU B 109 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   PHE B 111 " --> pdb=" O   GLY B  88 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   GLY B  88 " --> pdb=" O   PHE B 111 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 199 through 200
    Processing sheet with id=AA7, first strand: chain 'B' and resid 363 through 364
      removed outlier: 9.335A  pdb=" N   GLU B 364 " --> pdb=" O   TRP B 348 " (cutoff:3.500A)
      removed outlier: 6.944A  pdb=" N   PHE B 350 " --> pdb=" O   GLU B 364 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   TRP B 385 " --> pdb=" O   ILE B 332 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   CYS B 382 " --> pdb=" O   ILE B 397 " (cutoff:3.500A)
      removed outlier: 8.160A  pdb=" N   CYS B 399 " --> pdb=" O   CYS B 382 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   PHE B 384 " --> pdb=" O   CYS B 399 " (cutoff:3.500A)
      removed outlier: 7.902A  pdb=" N   PHE B 401 " --> pdb=" O   PHE B 384 " (cutoff:3.500A)
      removed outlier: 6.858A  pdb=" N   SER B 396 " --> pdb=" O   TYR B 511 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 410 through 412
    Processing sheet with id=AA9, first strand: chain 'B' and resid 446 through 447
      removed outlier: 6.455A  pdb=" N   TYR B 446 " --> pdb=" O   ILE B 474 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9

    168 hydrogen bonds defined for protein.
    456 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      19 hydrogen bonds
      38 hydrogen bond angles
      0 basepair planarities
      8 basepair parallelities
      13 stacking parallelities
  Total time for adding SS restraints: 1.00

  Time building geometry restraints manager: 0.48 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1645
        1.34 -     1.46: 1154
        1.46 -     1.57: 2714
        1.57 -     1.69: 31
        1.69 -     1.81: 68
  Bond restraints: 5612
  Sorted by residual:
  bond pdb=" O10 K5X E 101 "
       pdb=" P09 K5X E 101 "
    ideal  model  delta    sigma   weight residual
    1.668  1.516  0.152 2.00e-02 2.50e+03 5.78e+01
  bond pdb=" O1  K5X E 101 "
       pdb=" P09 K5X E 101 "
    ideal  model  delta    sigma   weight residual
    1.669  1.522  0.147 2.00e-02 2.50e+03 5.43e+01
  bond pdb=" N   ASN A  62 "
       pdb=" CA  ASN A  62 "
    ideal  model  delta    sigma   weight residual
    1.454  1.490 -0.036 1.17e-02 7.31e+03 9.46e+00
  bond pdb=" N  BASN B 266 "
       pdb=" CA BASN B 266 "
    ideal  model  delta    sigma   weight residual
    1.456  1.492 -0.036 1.27e-02 6.20e+03 7.98e+00
  bond pdb=" C18 K5X E 101 "
       pdb=" N20 K5X E 101 "
    ideal  model  delta    sigma   weight residual
    1.437  1.381  0.056 2.00e-02 2.50e+03 7.81e+00
  ... (remaining 5607 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    12.16: 7705
       12.16 -    24.33: 0
       24.33 -    36.49: 0
       36.49 -    48.65: 0
       48.65 -    60.82: 1
  Bond angle restraints: 7706
  Sorted by residual:
  angle pdb=" O1  K5X E 101 "
        pdb=" P09 K5X E 101 "
        pdb=" O10 K5X E 101 "
      ideal   model   delta    sigma   weight residual
      54.51  115.33  -60.82 3.00e+00 1.11e-01 4.11e+02
  angle pdb=" C   ARG B  98 "
        pdb=" CA  ARG B  98 "
        pdb=" CB  ARG B  98 "
      ideal   model   delta    sigma   weight residual
     117.23  111.14    6.09 1.36e+00 5.41e-01 2.00e+01
  angle pdb=" O5'   G E   9 "
        pdb=" C5'   G E   9 "
        pdb=" C4'   G E   9 "
      ideal   model   delta    sigma   weight residual
     109.40  112.56   -3.16 8.00e-01 1.56e+00 1.56e+01
  angle pdb=" C06 K5X E 101 "
        pdb=" C04 K5X E 101 "
        pdb=" O05 K5X E 101 "
      ideal   model   delta    sigma   weight residual
     105.37  115.93  -10.56 3.00e+00 1.11e-01 1.24e+01
  angle pdb=" O5'   U E  11 "
        pdb=" C5'   U E  11 "
        pdb=" C4'   U E  11 "
      ideal   model   delta    sigma   weight residual
     109.40  112.07   -2.67 8.00e-01 1.56e+00 1.11e+01
  ... (remaining 7701 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.09: 3165
       24.09 -    48.18: 123
       48.18 -    72.27: 30
       72.27 -    96.36: 5
       96.36 -   120.45: 1
  Dihedral angle restraints: 3324
    sinusoidal: 1437
      harmonic: 1887
  Sorted by residual:
  dihedral pdb=" O08 K5X E 101 "
           pdb=" C06 K5X E 101 "
           pdb=" C07 K5X E 101 "
           pdb=" O13 K5X E 101 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -67.06   53.39 -120.45     1      3.00e+01 1.11e-03 1.61e+01
  dihedral pdb=" CA BVAL B 269 "
           pdb=" C  BVAL B 269 "
           pdb=" N  BALA B 270 "
           pdb=" CA BALA B 270 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.28  -16.72     0      5.00e+00 4.00e-02 1.12e+01
  dihedral pdb=" CA  SER B 396 "
           pdb=" C   SER B 396 "
           pdb=" N   ILE B 397 "
           pdb=" CA  ILE B 397 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.31   16.69     0      5.00e+00 4.00e-02 1.11e+01
  ... (remaining 3321 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.088: 779
       0.088 -    0.177: 77
       0.177 -    0.265: 2
       0.265 -    0.354: 0
       0.354 -    0.442: 1
  Chirality restraints: 859
  Sorted by residual:
  chirality pdb=" C04 K5X E 101 "
            pdb=" C02 K5X E 101 "
            pdb=" C06 K5X E 101 "
            pdb=" O05 K5X E 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.90   -2.46   -0.44 2.00e-01 2.50e+01 4.89e+00
  chirality pdb=" CA  GLN B 145 "
            pdb=" N   GLN B 145 "
            pdb=" C   GLN B 145 "
            pdb=" CB  GLN B 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 8.76e-01
  chirality pdb=" C14 K5X E 101 "
            pdb=" C02 K5X E 101 "
            pdb=" N15 K5X E 101 "
            pdb=" O13 K5X E 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.59    2.41    0.18 2.00e-01 2.50e+01 8.41e-01
  ... (remaining 856 not shown)

  Planarity restraints: 928
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  78 "    0.193 9.50e-02 1.11e+02   8.66e-02 4.61e+00
        pdb=" NE  ARG A  78 "   -0.012 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  78 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  78 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  78 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS B  19 "    0.029 5.00e-02 4.00e+02   4.39e-02 3.08e+00
        pdb=" N   PRO B  20 "   -0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO B  20 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B  20 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B 354 "   -0.029 5.00e-02 4.00e+02   4.34e-02 3.02e+00
        pdb=" N   PRO B 355 "    0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO B 355 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 355 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 925 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 42
        2.62 -     3.19: 4517
        3.19 -     3.76: 8468
        3.76 -     4.33: 12407
        4.33 -     4.90: 19936
  Nonbonded interactions: 45370
  Sorted by model distance:
  nonbonded pdb=" NE2 HIS B 257 "
            pdb="ZN    ZN B 603 "
     model   vdw
     2.053 2.310
  nonbonded pdb=" OD2 ASP B  90 "
            pdb="MG    MG B 601 "
     model   vdw
     2.057 2.170
  nonbonded pdb=" OE2 GLU B  92 "
            pdb="MG    MG B 601 "
     model   vdw
     2.084 2.170
  nonbonded pdb=" OD2 ASP B 273 "
            pdb="MG    MG B 601 "
     model   vdw
     2.106 2.170
  nonbonded pdb=" ND1AHIS B 264 "
            pdb="ZN    ZN B 603 "
     model   vdw
     2.135 2.310
  ... (remaining 45365 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.48 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.590
  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:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     8.200
  Find NCS groups from input model:        0.010
  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:7.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
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   0.152   5629  Z= 0.296
  Angle     :  0.991  60.818   7721  Z= 0.494
  Chirality :  0.052   0.442    859
  Planarity :  0.006   0.087    928
  Dihedral  : 13.685 120.453   2112
  Min Nonbonded Distance : 2.053

Molprobity Statistics.
  All-atom Clashscore : 2.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.52 (0.33), residues: 644
  helix: -0.41 (0.39), residues: 164
  sheet: -0.57 (0.55), residues: 87
  loop : -0.16 (0.32), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  78 
 TYR   0.010   0.002   TYR B 420 
 PHE   0.013   0.002   PHE B 198 
 TRP   0.010   0.001   TRP A 123 
 HIS   0.008   0.001   HIS B 283 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00548 /  0.29 ( 5612)
  covalent geometry    : angle       0.98431 /  0.49 ( 7706)
  hydrogen bonds       : bond        0.14848 / 10.64 (  182)
  hydrogen bonds       : angle       6.31248 /  4.52 (  494)
  metal coordination   : bond        0.00597 /  0.39 (   16)
  metal coordination   : angle       2.80177 /  1.95 (   15)
  Misc. bond           : bond        0.04007 /  2.11 (    1)

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

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

  1288 Ramachandran restraints generated.
    644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1288 Ramachandran restraints generated.
    644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.130 
Fit side-chains
REVERT: B   65 GLN cc_start: 0.7665 (mm-40) cc_final: 0.7459 (mm-40)
REVERT: B  147 LYS cc_start: 0.8099 (mtpt) cc_final: 0.7843 (mtpt)
REVERT: B  241 MET cc_start: 0.8527 (ptp) cc_final: 0.8302 (ptp)
REVERT: B  328 VAL cc_start: 0.9044 (p) cc_final: 0.8831 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.5948
  time to fit residues: 83.3215
Evaluate side-chains
  104 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   chunk 62 optimal weight:    0.4980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 64 optimal weight:    4.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  22 GLN
B 246 GLN
B 254 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.123876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.103765 restraints weight = 27803.732|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 3.39
r_work: 0.3216 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3220
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3220 r_free = 0.3220    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3220 r_free = 0.3220    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (7 function evaluations)
r_final: 0.3220
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8355
moved from start:          0.1109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   5629  Z= 0.214
  Angle     :  0.581   6.670   7721  Z= 0.299
  Chirality :  0.045   0.151    859
  Planarity :  0.005   0.050    928
  Dihedral  : 12.169 127.782    962
  Min Nonbonded Distance : 1.959

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 11.87 %
    Favored  : 86.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.19 (0.33), residues: 644
  helix:  0.18 (0.41), residues: 163
  sheet: -0.60 (0.54), residues: 87
  loop : -0.04 (0.32), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 476 
 TYR   0.012   0.002   TYR B  51 
 PHE   0.010   0.002   PHE A  16 
 TRP   0.009   0.001   TRP A 123 
 HIS   0.008   0.001   HIS B 283 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00512 /  0.21 ( 5612)
  covalent geometry    : angle       0.56758 /  0.30 ( 7706)
  hydrogen bonds       : bond        0.04779 /  3.30 (  182)
  hydrogen bonds       : angle       4.84355 /  3.45 (  494)
  metal coordination   : bond        0.00983 /  0.56 (   16)
  metal coordination   : angle       2.89535 /  1.93 (   15)
  Misc. bond           : bond        0.00195 /  0.10 (    1)

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

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

  1288 Ramachandran restraints generated.
    644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1288 Ramachandran restraints generated.
    644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 105
  time to evaluate  : 0.164 
Fit side-chains
REVERT: A   53 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.8402 (mt0)
REVERT: A   65 GLN cc_start: 0.8794 (mt0) cc_final: 0.8515 (mt0)
REVERT: B  328 VAL cc_start: 0.9018 (p) cc_final: 0.8815 (t)
REVERT: B  334 ASN cc_start: 0.8034 (t0) cc_final: 0.7775 (t160)
  outliers start: 7
  outliers final: 2
  residues processed: 106
  average time/residue: 0.5846
  time to fit residues: 64.3950
Evaluate side-chains
  107 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 104
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 GLN
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain B residue   75 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 42 optimal weight:    0.0060
   chunk 11 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 5 optimal weight:    0.6980
   chunk 51 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9990
   chunk 43 optimal weight:    0.8980
   chunk 28 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9990
   chunk 16 optimal weight:    0.4980
   overall best weight:    0.4996

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  71 ASN
B 246 GLN
B 254 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.124291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.104238 restraints weight = 27796.568|
|-----------------------------------------------------------------------------|
r_work (start): 0.3419 rms_B_bonded: 3.39
r_work: 0.3226 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3228
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3228 r_free = 0.3228    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3228 r_free = 0.3228    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3228
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8344
moved from start:          0.1346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   5629  Z= 0.153
  Angle     :  0.523   6.427   7721  Z= 0.269
  Chirality :  0.042   0.151    859
  Planarity :  0.004   0.056    928
  Dihedral  : 11.533 115.792    962
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 2.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 14.21 %
    Favored  : 83.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.01 (0.33), residues: 644
  helix:  0.50 (0.41), residues: 163
  sheet: -0.45 (0.56), residues: 83
  loop : -0.01 (0.32), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 476 
 TYR   0.012   0.001   TYR B 498 
 PHE   0.011   0.001   PHE B 326 
 TRP   0.009   0.001   TRP A 123 
 HIS   0.005   0.001   HIS B 283 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00366 /  0.15 ( 5612)
  covalent geometry    : angle       0.50984 /  0.27 ( 7706)
  hydrogen bonds       : bond        0.04110 /  2.82 (  182)
  hydrogen bonds       : angle       4.59227 /  3.25 (  494)
  metal coordination   : bond        0.00648 /  0.39 (   16)
  metal coordination   : angle       2.68588 /  1.81 (   15)
  Misc. bond           : bond        0.00072 /  0.04 (    1)

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

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

  1288 Ramachandran restraints generated.
    644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1288 Ramachandran restraints generated.
    644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 0.117 
Fit side-chains
REVERT: B   47 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8788 (pttp)
REVERT: B  328 VAL cc_start: 0.9020 (p) cc_final: 0.8797 (t)
REVERT: B  334 ASN cc_start: 0.8031 (t0) cc_final: 0.7716 (t160)
  outliers start: 10
  outliers final: 4
  residues processed: 107
  average time/residue: 0.6326
  time to fit residues: 70.5085
Evaluate side-chains
  109 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 104
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain B residue   47 LYS
Chi-restraints excluded: chain B residue  145 GLN
Chi-restraints excluded: chain B residue  513 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 0 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   chunk 61 optimal weight:    0.8980
   chunk 42 optimal weight:    0.1980
   chunk 34 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 60 optimal weight:    0.2980
   chunk 62 optimal weight:    0.8980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 254 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.123417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.104373 restraints weight = 20016.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 2.85
r_work: 0.3261 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3250
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3250 r_free = 0.3250    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3250 r_free = 0.3250    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3250
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.1468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5629  Z= 0.174
  Angle     :  0.535   6.466   7721  Z= 0.275
  Chirality :  0.043   0.149    859
  Planarity :  0.005   0.058    928
  Dihedral  : 10.926  91.028    962
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 13.67 %
    Favored  : 84.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.11 (0.33), residues: 644
  helix:  0.70 (0.41), residues: 163
  sheet: -0.46 (0.58), residues: 77
  loop :  0.01 (0.32), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 476 
 TYR   0.010   0.001   TYR B 420 
 PHE   0.011   0.001   PHE B 133 
 TRP   0.009   0.001   TRP A 123 
 HIS   0.006   0.001   HIS B 283 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00421 /  0.17 ( 5612)
  covalent geometry    : angle       0.52194 /  0.27 ( 7706)
  hydrogen bonds       : bond        0.04037 /  2.76 (  182)
  hydrogen bonds       : angle       4.54632 /  3.20 (  494)
  metal coordination   : bond        0.00809 /  0.47 (   16)
  metal coordination   : angle       2.71742 /  1.82 (   15)
  Misc. bond           : bond        0.00008 /  0.00 (    1)

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

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

  1288 Ramachandran restraints generated.
    644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1288 Ramachandran restraints generated.
    644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 0.198 
Fit side-chains
REVERT: A   65 GLN cc_start: 0.8718 (mt0) cc_final: 0.8429 (mt0)
REVERT: B   47 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8770 (pttp)
REVERT: B  144 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7875 (m-30)
REVERT: B  328 VAL cc_start: 0.9024 (p) cc_final: 0.8797 (t)
  outliers start: 12
  outliers final: 5
  residues processed: 106
  average time/residue: 0.6445
  time to fit residues: 70.9967
Evaluate side-chains
  109 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 102
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain A residue   63 MET
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain B residue   47 LYS
Chi-restraints excluded: chain B residue  144 ASP
Chi-restraints excluded: chain B residue  145 GLN
Chi-restraints excluded: chain B residue  513 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 44 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   chunk 29 optimal weight:    0.5980
   chunk 62 optimal weight:    0.1980
   chunk 3 optimal weight:    0.9990
   chunk 57 optimal weight:    0.4980
   chunk 21 optimal weight:    0.7980
   chunk 32 optimal weight:    0.7980
   chunk 51 optimal weight:    0.5980
   chunk 52 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 246 GLN
B 254 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.121405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.103785 restraints weight = 15106.587|
|-----------------------------------------------------------------------------|
r_work (start): 0.3446 rms_B_bonded: 2.35
r_work: 0.3301 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3132 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3138
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3138 r_free = 0.3138    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3138 r_free = 0.3138    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3138
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8411
moved from start:          0.1595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5629  Z= 0.160
  Angle     :  0.518   6.295   7721  Z= 0.266
  Chirality :  0.043   0.151    859
  Planarity :  0.004   0.054    928
  Dihedral  : 10.628  76.902    962
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 13.31 %
    Favored  : 84.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.17 (0.33), residues: 644
  helix:  0.86 (0.42), residues: 163
  sheet: -0.56 (0.57), residues: 77
  loop :  0.02 (0.32), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 476 
 TYR   0.010   0.001   TYR B  51 
 PHE   0.009   0.001   PHE A  68 
 TRP   0.008   0.001   TRP A 123 
 HIS   0.004   0.001   HIS B 283 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00387 /  0.16 ( 5612)
  covalent geometry    : angle       0.50497 /  0.26 ( 7706)
  hydrogen bonds       : bond        0.03902 /  2.66 (  182)
  hydrogen bonds       : angle       4.48311 /  3.16 (  494)
  metal coordination   : bond        0.00732 /  0.42 (   16)
  metal coordination   : angle       2.69792 /  1.82 (   15)
  Misc. bond           : bond        0.00038 /  0.02 (    1)

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

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

  1288 Ramachandran restraints generated.
    644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1288 Ramachandran restraints generated.
    644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.199 
Fit side-chains
REVERT: A   65 GLN cc_start: 0.8815 (mt0) cc_final: 0.8527 (mt0)
REVERT: B  144 ASP cc_start: 0.8381 (OUTLIER) cc_final: 0.8124 (m-30)
REVERT: B  328 VAL cc_start: 0.9099 (p) cc_final: 0.8852 (t)
  outliers start: 10
  outliers final: 4
  residues processed: 104
  average time/residue: 0.6381
  time to fit residues: 69.0177
Evaluate side-chains
  107 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 102
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain B residue  144 ASP
Chi-restraints excluded: chain B residue  145 GLN
Chi-restraints excluded: chain B residue  513 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 63 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0000
   chunk 1 optimal weight:    0.5980
   chunk 3 optimal weight:    0.6980
   chunk 31 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9990
   chunk 58 optimal weight:    5.9990
   chunk 36 optimal weight:    0.3980
   chunk 24 optimal weight:    0.0670
   overall best weight:    0.3322

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  95 HIS
B 245 GLN
B 246 GLN
B 254 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.122203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.103226 restraints weight = 22744.720|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 2.99
r_work: 0.3266 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3257
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3257 r_free = 0.3257    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3257 r_free = 0.3257    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3257
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.1665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5629  Z= 0.118
  Angle     :  0.498   5.976   7721  Z= 0.255
  Chirality :  0.041   0.149    859
  Planarity :  0.004   0.056    928
  Dihedral  : 10.553  73.434    962
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 14.39 %
    Favored  : 84.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.24 (0.34), residues: 644
  helix:  1.04 (0.42), residues: 163
  sheet: -0.57 (0.56), residues: 83
  loop :  0.05 (0.32), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B 476 
 TYR   0.011   0.001   TYR B 498 
 PHE   0.008   0.001   PHE B 426 
 TRP   0.008   0.001   TRP B 227 
 HIS   0.003   0.001   HIS B 283 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00278 /  0.12 ( 5612)
  covalent geometry    : angle       0.48683 /  0.25 ( 7706)
  hydrogen bonds       : bond        0.03637 /  2.48 (  182)
  hydrogen bonds       : angle       4.37822 /  3.10 (  494)
  metal coordination   : bond        0.00519 /  0.31 (   16)
  metal coordination   : angle       2.45098 /  1.66 (   15)
  Misc. bond           : bond        0.00028 /  0.01 (    1)

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

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

  1288 Ramachandran restraints generated.
    644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1288 Ramachandran restraints generated.
    644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 103
  time to evaluate  : 0.194 
Fit side-chains
REVERT: A   65 GLN cc_start: 0.8693 (mt0) cc_final: 0.8413 (mt0)
REVERT: B  328 VAL cc_start: 0.9014 (p) cc_final: 0.8776 (t)
  outliers start: 7
  outliers final: 4
  residues processed: 105
  average time/residue: 0.5540
  time to fit residues: 60.5868
Evaluate side-chains
  106 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 102
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain B residue  145 GLN
Chi-restraints excluded: chain B residue  513 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 8 optimal weight:    5.9990
   chunk 9 optimal weight:    0.5980
   chunk 7 optimal weight:    0.6980
   chunk 1 optimal weight:    0.5980
   chunk 59 optimal weight:    0.9990
   chunk 49 optimal weight:    0.4980
   chunk 32 optimal weight:    0.6980
   chunk 53 optimal weight:    3.9990
   chunk 58 optimal weight:    5.9990
   chunk 33 optimal weight:    0.8980
   chunk 4 optimal weight:    0.3980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 245 GLN
B 254 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.121460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.103217 restraints weight = 18306.473|
|-----------------------------------------------------------------------------|
r_work (start): 0.3436 rms_B_bonded: 2.63
r_work: 0.3279 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3284
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3284 r_free = 0.3284    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3284 r_free = 0.3284    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (7 function evaluations)
r_final: 0.3284
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8306
moved from start:          0.1711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   5629  Z= 0.163
  Angle     :  0.520   8.733   7721  Z= 0.263
  Chirality :  0.042   0.149    859
  Planarity :  0.004   0.055    928
  Dihedral  : 10.530  73.387    962
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 14.75 %
    Favored  : 83.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.22 (0.34), residues: 644
  helix:  1.00 (0.42), residues: 163
  sheet: -0.59 (0.56), residues: 83
  loop :  0.04 (0.32), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 476 
 TYR   0.010   0.001   TYR B 420 
 PHE   0.010   0.001   PHE A  68 
 TRP   0.008   0.001   TRP A 123 
 HIS   0.005   0.001   HIS B 283 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00396 /  0.16 ( 5612)
  covalent geometry    : angle       0.50739 /  0.26 ( 7706)
  hydrogen bonds       : bond        0.03789 /  2.56 (  182)
  hydrogen bonds       : angle       4.35252 /  3.08 (  494)
  metal coordination   : bond        0.00774 /  0.44 (   16)
  metal coordination   : angle       2.63106 /  1.78 (   15)
  Misc. bond           : bond        0.00038 /  0.02 (    1)

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

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

  1288 Ramachandran restraints generated.
    644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1288 Ramachandran restraints generated.
    644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 105
  time to evaluate  : 0.205 
Fit side-chains
REVERT: A   65 GLN cc_start: 0.8688 (mt0) cc_final: 0.8410 (mt0)
REVERT: B   47 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8725 (ptmm)
REVERT: B  328 VAL cc_start: 0.9001 (p) cc_final: 0.8754 (t)
  outliers start: 8
  outliers final: 6
  residues processed: 107
  average time/residue: 0.6405
  time to fit residues: 71.3047
Evaluate side-chains
  111 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 104
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain B residue   47 LYS
Chi-restraints excluded: chain B residue  144 ASP
Chi-restraints excluded: chain B residue  145 GLN
Chi-restraints excluded: chain B residue  388 ASN
Chi-restraints excluded: chain B residue  513 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 35 optimal weight:    4.9990
   chunk 11 optimal weight:    0.5980
   chunk 26 optimal weight:    0.8980
   chunk 3 optimal weight:    0.0050
   chunk 47 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 58 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9980
   chunk 44 optimal weight:    0.6980
   chunk 53 optimal weight:    3.9990
   overall best weight:    0.6394

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 245 GLN
B 254 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.120848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.101654 restraints weight = 23302.406|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 3.03
r_work: 0.3245 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3247
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3247 r_free = 0.3247    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3247 r_free = 0.3247    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3247
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.1730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5629  Z= 0.181
  Angle     :  0.530   8.313   7721  Z= 0.268
  Chirality :  0.043   0.149    859
  Planarity :  0.004   0.062    928
  Dihedral  : 10.524  73.405    962
  Min Nonbonded Distance : 1.931

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 14.93 %
    Favored  : 83.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.20 (0.33), residues: 644
  helix:  0.98 (0.42), residues: 163
  sheet: -0.60 (0.57), residues: 77
  loop :  0.02 (0.32), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 476 
 TYR   0.011   0.002   TYR B 420 
 PHE   0.016   0.001   PHE B 326 
 TRP   0.008   0.001   TRP A 123 
 HIS   0.005   0.001   HIS B 283 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00440 /  0.18 ( 5612)
  covalent geometry    : angle       0.51641 /  0.27 ( 7706)
  hydrogen bonds       : bond        0.03917 /  2.65 (  182)
  hydrogen bonds       : angle       4.34706 /  3.06 (  494)
  metal coordination   : bond        0.00820 /  0.46 (   16)
  metal coordination   : angle       2.72670 /  1.85 (   15)
  Misc. bond           : bond        0.00036 /  0.02 (    1)

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

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

  1288 Ramachandran restraints generated.
    644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1288 Ramachandran restraints generated.
    644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 0.246 
Fit side-chains
REVERT: A   65 GLN cc_start: 0.8714 (mt0) cc_final: 0.8392 (mt0)
REVERT: B   47 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8753 (ptmm)
REVERT: B  160 ASN cc_start: 0.8233 (p0) cc_final: 0.8021 (p0)
REVERT: B  328 VAL cc_start: 0.9011 (p) cc_final: 0.8772 (t)
  outliers start: 10
  outliers final: 5
  residues processed: 108
  average time/residue: 0.6183
  time to fit residues: 69.5724
Evaluate side-chains
  111 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 105
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain B residue   47 LYS
Chi-restraints excluded: chain B residue  145 GLN
Chi-restraints excluded: chain B residue  388 ASN
Chi-restraints excluded: chain B residue  513 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 21 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   chunk 53 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 17 optimal weight:    0.0770
   chunk 3 optimal weight:    0.0020
   chunk 61 optimal weight:    0.5980
   chunk 46 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.3946

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 245 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.122447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.104359 restraints weight = 17480.675|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 2.56
r_work: 0.3292 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3281
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3281 r_free = 0.3281    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3281 r_free = 0.3281    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3281
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8295
moved from start:          0.1780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   5629  Z= 0.129
  Angle     :  0.513   8.392   7721  Z= 0.260
  Chirality :  0.042   0.148    859
  Planarity :  0.004   0.062    928
  Dihedral  : 10.522  73.448    962
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 15.47 %
    Favored  : 83.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.27 (0.33), residues: 644
  helix:  1.11 (0.42), residues: 163
  sheet: -0.64 (0.58), residues: 77
  loop :  0.04 (0.32), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 476 
 TYR   0.010   0.001   TYR B 420 
 PHE   0.014   0.001   PHE B 326 
 TRP   0.008   0.001   TRP B 227 
 HIS   0.003   0.001   HIS B 283 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00306 /  0.13 ( 5612)
  covalent geometry    : angle       0.50104 /  0.26 ( 7706)
  hydrogen bonds       : bond        0.03702 /  2.50 (  182)
  hydrogen bonds       : angle       4.29363 /  3.02 (  494)
  metal coordination   : bond        0.00554 /  0.33 (   16)
  metal coordination   : angle       2.55915 /  1.75 (   15)
  Misc. bond           : bond        0.00020 /  0.01 (    1)

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

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

  1288 Ramachandran restraints generated.
    644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1288 Ramachandran restraints generated.
    644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 105
  time to evaluate  : 0.201 
Fit side-chains
REVERT: A   65 GLN cc_start: 0.8674 (mt0) cc_final: 0.8406 (mt0)
REVERT: B   47 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8732 (ptmm)
REVERT: B  160 ASN cc_start: 0.8180 (p0) cc_final: 0.7975 (p0)
REVERT: B  328 VAL cc_start: 0.8946 (p) cc_final: 0.8702 (t)
  outliers start: 7
  outliers final: 5
  residues processed: 106
  average time/residue: 0.6147
  time to fit residues: 67.8827
Evaluate side-chains
  110 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 104
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain B residue   47 LYS
Chi-restraints excluded: chain B residue  144 ASP
Chi-restraints excluded: chain B residue  388 ASN
Chi-restraints excluded: chain B residue  513 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 50 optimal weight:    0.9980
   chunk 47 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0010
   chunk 33 optimal weight:    0.9980
   chunk 25 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0070
   chunk 54 optimal weight:    0.1980
   chunk 61 optimal weight:    0.1980
   chunk 12 optimal weight:    0.0470
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.0902

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.125928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.106808 restraints weight = 21108.270|
|-----------------------------------------------------------------------------|
r_work (start): 0.3459 rms_B_bonded: 2.93
r_work: 0.3290 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3294
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3294 r_free = 0.3294    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3294 r_free = 0.3294    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3294
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.1887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   5629  Z= 0.085
  Angle     :  0.475   8.298   7721  Z= 0.242
  Chirality :  0.040   0.145    859
  Planarity :  0.004   0.058    928
  Dihedral  : 10.473  73.497    962
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 16.73 %
    Favored  : 82.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.44 (0.34), residues: 644
  helix:  1.58 (0.42), residues: 157
  sheet: -0.91 (0.58), residues: 77
  loop :  0.11 (0.32), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 476 
 TYR   0.010   0.001   TYR B 420 
 PHE   0.010   0.001   PHE B 326 
 TRP   0.010   0.001   TRP B 227 
 HIS   0.002   0.000   HIS B 427 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00188 /  0.09 ( 5612)
  covalent geometry    : angle       0.46645 /  0.24 ( 7706)
  hydrogen bonds       : bond        0.03120 /  2.09 (  182)
  hydrogen bonds       : angle       4.13517 /  2.95 (  494)
  metal coordination   : bond        0.00324 /  0.21 (   16)
  metal coordination   : angle       2.07075 /  1.46 (   15)
  Misc. bond           : bond        0.00015 /  0.01 (    1)

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

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

  1288 Ramachandran restraints generated.
    644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1288 Ramachandran restraints generated.
    644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 106
  time to evaluate  : 0.198 
Fit side-chains
REVERT: A   65 GLN cc_start: 0.8612 (mt0) cc_final: 0.8334 (mt0)
REVERT: B   47 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8707 (ptmm)
REVERT: B  328 VAL cc_start: 0.8993 (p) cc_final: 0.8748 (t)
  outliers start: 5
  outliers final: 3
  residues processed: 108
  average time/residue: 0.6079
  time to fit residues: 68.3023
Evaluate side-chains
  104 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 100
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain B residue   47 LYS
Chi-restraints excluded: chain B residue  388 ASN
Chi-restraints excluded: chain B residue  513 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 26 optimal weight:    0.0070
   chunk 33 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   chunk 31 optimal weight:    0.0870
   chunk 44 optimal weight:    0.5980
   chunk 57 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   chunk 22 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.4576

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 108 GLN
B 245 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.124953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.107561 restraints weight = 12891.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.3458 rms_B_bonded: 2.20
r_work: 0.3325 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3171 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3181
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3181 r_free = 0.3181    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3181 r_free = 0.3181    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3181
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.1893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   5629  Z= 0.143
  Angle     :  0.504   8.282   7721  Z= 0.257
  Chirality :  0.041   0.147    859
  Planarity :  0.004   0.061    928
  Dihedral  : 10.463  73.464    962
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 16.91 %
    Favored  : 82.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.33 (0.33), residues: 644
  helix:  1.28 (0.42), residues: 163
  sheet: -0.76 (0.58), residues: 75
  loop :  0.05 (0.32), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 476 
 TYR   0.010   0.001   TYR B 420 
 PHE   0.021   0.001   PHE B 326 
 TRP   0.008   0.001   TRP B 227 
 HIS   0.004   0.001   HIS B 283 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00350 /  0.14 ( 5612)
  covalent geometry    : angle       0.49369 /  0.26 ( 7706)
  hydrogen bonds       : bond        0.03475 /  2.32 (  182)
  hydrogen bonds       : angle       4.19375 /  2.98 (  494)
  metal coordination   : bond        0.00671 /  0.38 (   16)
  metal coordination   : angle       2.31371 /  1.58 (   15)
  Misc. bond           : bond        0.00019 /  0.01 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2619.31 seconds
wall clock time: 45 minutes 24.20 seconds (2724.20 seconds total)