Starting phenix.real_space_refine
on Thu Jul  2 01:56:33 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9yro_73372/07_2026/9yro_73372.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9yro_73372/07_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9yro_73372/07_2026/9yro_73372.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9yro_73372/07_2026/9yro_73372.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9yro_73372/07_2026/9yro_73372.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9yro_73372/07_2026/9yro_73372.map"
  }
  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-dev-6108/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: 1.62, per 1000 atoms: 0.30
  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: 0.36
  Conformation dependent library (CDL) restraints added in 302.6 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: 0.47
  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: 0.89

  Time building geometry restraints manager: 0.46 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=" 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=" C  BASN B 266 "
        pdb=" CA BASN B 266 "
        pdb=" CB BASN B 266 "
      ideal   model   delta    sigma   weight residual
     109.99  114.99   -5.00 1.61e+00 3.86e-01 9.66e+00
  angle pdb=" CA  ARG B  98 "
        pdb=" C   ARG B  98 "
        pdb=" N   GLU B  99 "
      ideal   model   delta    sigma   weight residual
     119.98  117.39    2.59 8.50e-01 1.38e+00 9.28e+00
  ... (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: 795
       0.088 -    0.177: 61
       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:             1.350
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.070
  Find NCS groups from input model:        0.030
  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:             0.000
  Load rotamer database and sin/cos tables:5.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.330
-------------------------------------------------------------------------------
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      :  0.005   0.152   5629  Z= 0.294
  Angle     :  0.973  60.818   7721  Z= 0.473
  Chirality :  0.049   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        0.00546 /  0.29 ( 5612)
  covalent geometry    : angle       0.96613 /  0.47 ( 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  : 0.145 
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: 0.4653
  time to fit residues: 65.2763
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  : 0.114 
-------------------------------------------------------------------------------
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:    3.9990
   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 = 0.3676 r_free = 0.3676 target = 0.123548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.103426 restraints weight = 27589.067|
|-----------------------------------------------------------------------------|
r_work (start): 0.3408 rms_B_bonded: 3.37
r_work: 0.3214 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3219
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3219 r_free = 0.3219    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 = 0.3219 r_free = 0.3219    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: 0.3219
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.1131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   5629  Z= 0.216
  Angle     :  0.582   6.730   7721  Z= 0.298
  Chirality :  0.045   0.152    859
  Planarity :  0.005   0.050    928
  Dihedral  : 12.127 128.593    962
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 2.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 11.87 %
    Favored  : 86.69 %
  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:  0.16 (0.41), residues: 163
  sheet: -0.59 (0.55), residues: 87
  loop : -0.05 (0.32), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 476 
 TYR   0.012   0.002   TYR B 237 
 PHE   0.011   0.002   PHE B 523 
 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        0.00520 /  0.22 ( 5612)
  covalent geometry    : angle       0.56771 /  0.30 ( 7706)
  hydrogen bonds       : bond        0.04674 /  3.23 (  182)
  hydrogen bonds       : angle       4.81892 /  3.44 (  494)
  metal coordination   : bond        0.00944 /  0.54 (   16)
  metal coordination   : angle       2.91747 /  1.94 (   15)
  Misc. bond           : bond        0.00024 /  0.01 (    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
  114 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 106
  time to evaluate  : 0.130 
Fit side-chains
REVERT: A   53 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8403 (mt0)
REVERT: B  334 ASN cc_start: 0.8029 (t0) cc_final: 0.7730 (t160)
  outliers start: 8
  outliers final: 3
  residues processed: 107
  average time/residue: 0.4177
  time to fit residues: 46.6630
Evaluate side-chains
  108 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 104
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain B residue  144 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 43 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 57 optimal weight:    0.0980
   chunk 16 optimal weight:    0.2980
   overall best weight:    0.4980

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.121687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.101967 restraints weight = 28002.790|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 3.34
r_work: 0.3230 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3218
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3218 r_free = 0.3218    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3218 r_free = 0.3218    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3218
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.1340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   5629  Z= 0.152
  Angle     :  0.521   6.438   7721  Z= 0.267
  Chirality :  0.042   0.150    859
  Planarity :  0.004   0.056    928
  Dihedral  : 11.474 114.863    962
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 14.57 %
    Favored  : 83.63 %
  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:  0.02 (0.33), residues: 644
  helix:  0.48 (0.42), residues: 163
  sheet: -0.41 (0.59), residues: 77
  loop : -0.01 (0.32), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B 476 
 TYR   0.011   0.001   TYR B 498 
 PHE   0.009   0.001   PHE B 426 
 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        0.00362 /  0.15 ( 5612)
  covalent geometry    : angle       0.50782 /  0.27 ( 7706)
  hydrogen bonds       : bond        0.04081 /  2.80 (  182)
  hydrogen bonds       : angle       4.60225 /  3.25 (  494)
  metal coordination   : bond        0.00634 /  0.39 (   16)
  metal coordination   : angle       2.68739 /  1.81 (   15)
  Misc. bond           : bond        0.00021 /  0.01 (    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
  116 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 106
  time to evaluate  : 0.132 
Fit side-chains
REVERT: B   47 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8786 (pttp)
REVERT: B  328 VAL cc_start: 0.9016 (OUTLIER) cc_final: 0.8779 (t)
REVERT: B  334 ASN cc_start: 0.8023 (t0) cc_final: 0.7716 (t160)
  outliers start: 10
  outliers final: 4
  residues processed: 108
  average time/residue: 0.4926
  time to fit residues: 55.2968
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  : 0.136 
-------------------------------------------------------------------------------
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  328 VAL
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:    0.9980
   chunk 22 optimal weight:    0.6980
   chunk 61 optimal weight:    0.4980
   chunk 42 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 26 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 62 optimal weight:    0.5980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3674 r_free = 0.3674 target = 0.123316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.104351 restraints weight = 20049.608|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 2.83
r_work: 0.3257 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3244
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3244 r_free = 0.3244    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 = 0.3244 r_free = 0.3244    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: 0.3244
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
moved from start:          0.1496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   5629  Z= 0.192
  Angle     :  0.542   6.523   7721  Z= 0.278
  Chirality :  0.044   0.150    859
  Planarity :  0.005   0.060    928
  Dihedral  : 10.897  91.171    962
  Min Nonbonded Distance : 1.927

Molprobity Statistics.
  All-atom Clashscore : 3.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 13.85 %
    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:  0.09 (0.33), residues: 644
  helix:  0.65 (0.41), residues: 163
  sheet: -0.39 (0.59), residues: 77
  loop : -0.01 (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   0.011   0.002   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        0.00465 /  0.19 ( 5612)
  covalent geometry    : angle       0.52836 /  0.28 ( 7706)
  hydrogen bonds       : bond        0.04119 /  2.81 (  182)
  hydrogen bonds       : angle       4.55023 /  3.19 (  494)
  metal coordination   : bond        0.00885 /  0.51 (   16)
  metal coordination   : angle       2.78524 /  1.86 (   15)
  Misc. bond           : bond        0.00032 /  0.02 (    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  : 0.137 
Fit side-chains
REVERT: A   65 GLN cc_start: 0.8728 (mt0) cc_final: 0.8440 (mt0)
REVERT: B   47 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8773 (pttp)
REVERT: B  144 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7886 (m-30)
REVERT: B  328 VAL cc_start: 0.9025 (p) cc_final: 0.8787 (t)
  outliers start: 12
  outliers final: 4
  residues processed: 106
  average time/residue: 0.4747
  time to fit residues: 52.3987
Evaluate side-chains
  108 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 102
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
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  513 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 44 optimal weight:    0.5980
   chunk 20 optimal weight:    0.5980
   chunk 29 optimal weight:    0.5980
   chunk 62 optimal weight:    0.2980
   chunk 3 optimal weight:    0.6980
   chunk 57 optimal weight:    0.8980
   chunk 21 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   chunk 52 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.3681 r_free = 0.3681 target = 0.123787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.105695 restraints weight = 15056.385|
|-----------------------------------------------------------------------------|
r_work (start): 0.3443 rms_B_bonded: 2.41
r_work: 0.3295 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3283
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3283 r_free = 0.3283    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3283 r_free = 0.3283    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: 0.3283
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start:          0.1547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   5629  Z= 0.158
  Angle     :  0.516   6.315   7721  Z= 0.265
  Chirality :  0.043   0.152    859
  Planarity :  0.004   0.055    928
  Dihedral  : 10.618  77.928    962
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 3.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 13.13 %
    Favored  : 85.07 %
  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:  0.14 (0.33), residues: 644
  helix:  0.81 (0.42), residues: 163
  sheet: -0.43 (0.59), residues: 77
  loop : -0.01 (0.32), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 476 
 TYR   0.010   0.001   TYR B 420 
 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        0.00380 /  0.16 ( 5612)
  covalent geometry    : angle       0.50274 /  0.26 ( 7706)
  hydrogen bonds       : bond        0.03887 /  2.64 (  182)
  hydrogen bonds       : angle       4.49587 /  3.16 (  494)
  metal coordination   : bond        0.00718 /  0.41 (   16)
  metal coordination   : angle       2.70791 /  1.83 (   15)
  Misc. bond           : bond        0.00040 /  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
  114 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 104
  time to evaluate  : 0.189 
Fit side-chains
REVERT: A   65 GLN cc_start: 0.8687 (mt0) cc_final: 0.8414 (mt0)
REVERT: B   47 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8734 (pttp)
REVERT: B  144 ASP cc_start: 0.8075 (OUTLIER) cc_final: 0.7812 (m-30)
REVERT: B  160 ASN cc_start: 0.8191 (p0) cc_final: 0.7983 (p0)
REVERT: B  328 VAL cc_start: 0.8990 (OUTLIER) cc_final: 0.8748 (t)
  outliers start: 10
  outliers final: 4
  residues processed: 106
  average time/residue: 0.4908
  time to fit residues: 54.2869
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  : 0.204 
-------------------------------------------------------------------------------
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  328 VAL
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:    1.9990
   chunk 63 optimal weight:    0.1980
   chunk 21 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0870
   chunk 1 optimal weight:    0.6980
   chunk 3 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   chunk 58 optimal weight:    0.8980
   chunk 36 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.5158

-------------------------------------------------------------------------------
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 = 0.3665 r_free = 0.3665 target = 0.120977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.101866 restraints weight = 23286.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.3427 rms_B_bonded: 3.01
r_work: 0.3250 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3238
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3238 r_free = 0.3238    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 = 0.3238 r_free = 0.3238    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: 0.3238
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8331
moved from start:          0.1611

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= 0.155
  Angle     :  0.514   6.362   7721  Z= 0.263
  Chirality :  0.042   0.149    859
  Planarity :  0.004   0.058    928
  Dihedral  : 10.538  73.358    962
  Min Nonbonded Distance : 1.946

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 14.03 %
    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:  0.16 (0.33), residues: 644
  helix:  0.92 (0.42), residues: 163
  sheet: -0.52 (0.58), residues: 77
  loop : -0.02 (0.32), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B 476 
 TYR   0.010   0.001   TYR B 420 
 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        0.00375 /  0.16 ( 5612)
  covalent geometry    : angle       0.50103 /  0.26 ( 7706)
  hydrogen bonds       : bond        0.03842 /  2.61 (  182)
  hydrogen bonds       : angle       4.42898 /  3.11 (  494)
  metal coordination   : bond        0.00704 /  0.41 (   16)
  metal coordination   : angle       2.66401 /  1.80 (   15)
  Misc. bond           : bond        0.00038 /  0.02 (    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
  114 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 104
  time to evaluate  : 0.139 
Fit side-chains
REVERT: A   65 GLN cc_start: 0.8720 (mt0) cc_final: 0.8450 (mt0)
REVERT: B  144 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7908 (m-30)
REVERT: B  160 ASN cc_start: 0.8221 (p0) cc_final: 0.8011 (p0)
REVERT: B  328 VAL cc_start: 0.9016 (OUTLIER) cc_final: 0.8779 (t)
  outliers start: 10
  outliers final: 4
  residues processed: 107
  average time/residue: 0.4691
  time to fit residues: 52.1755
Evaluate side-chains
  113 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 107
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
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  328 VAL
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:    0.1980
   chunk 59 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9980
   chunk 32 optimal weight:    0.3980
   chunk 53 optimal weight:    0.9990
   chunk 58 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9980
   chunk 4 optimal weight:    0.0770
   overall best weight:    0.3938

-------------------------------------------------------------------------------
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 = 0.3678 r_free = 0.3678 target = 0.121936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.103730 restraints weight = 17874.212|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 2.59
r_work: 0.3289 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3278
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3278 r_free = 0.3278    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 = 0.3278 r_free = 0.3278    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: 0.3278
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
moved from start:          0.1663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5629  Z= 0.130
  Angle     :  0.509   8.006   7721  Z= 0.259
  Chirality :  0.042   0.149    859
  Planarity :  0.004   0.054    928
  Dihedral  : 10.513  73.366    962
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 15.11 %
    Favored  : 83.63 %
  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 (0.34), residues: 644
  helix:  0.99 (0.42), residues: 163
  sheet: -0.57 (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   0.009   0.001   PHE B 326 
 TRP   0.007   0.001   TRP B 159 
 HIS   0.003   0.001   HIS B 283 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00312 /  0.13 ( 5612)
  covalent geometry    : angle       0.49644 /  0.26 ( 7706)
  hydrogen bonds       : bond        0.03699 /  2.51 (  182)
  hydrogen bonds       : angle       4.38846 /  3.09 (  494)
  metal coordination   : bond        0.00583 /  0.35 (   16)
  metal coordination   : angle       2.56292 /  1.74 (   15)
  Misc. bond           : bond        0.00026 /  0.01 (    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: 7
    poor density    : 106
  time to evaluate  : 0.115 
Fit side-chains
REVERT: A   65 GLN cc_start: 0.8682 (mt0) cc_final: 0.8412 (mt0)
REVERT: B  160 ASN cc_start: 0.8181 (p0) cc_final: 0.7973 (p0)
REVERT: B  328 VAL cc_start: 0.8993 (OUTLIER) cc_final: 0.8748 (t)
  outliers start: 7
  outliers final: 4
  residues processed: 106
  average time/residue: 0.4534
  time to fit residues: 50.0301
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  : 0.125 
-------------------------------------------------------------------------------
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  328 VAL
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:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 26 optimal weight:    0.0970
   chunk 3 optimal weight:    0.0050
   chunk 47 optimal weight:    0.7980
   chunk 37 optimal weight:    0.6980
   chunk 58 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9990
   chunk 44 optimal weight:    0.5980
   chunk 53 optimal weight:    3.9990
   overall best weight:    0.4392

-------------------------------------------------------------------------------
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 = 0.3669 r_free = 0.3669 target = 0.121293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.102238 restraints weight = 23141.867|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 3.00
r_work: 0.3255 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3243
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3243 r_free = 0.3243    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 = 0.3243 r_free = 0.3243    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: 0.3243
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
moved from start:          0.1668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5629  Z= 0.137
  Angle     :  0.506   7.748   7721  Z= 0.257
  Chirality :  0.042   0.149    859
  Planarity :  0.004   0.059    928
  Dihedral  : 10.490  73.371    962
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 15.29 %
    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:  0.21 (0.34), residues: 644
  helix:  1.02 (0.42), residues: 163
  sheet: -0.62 (0.58), residues: 77
  loop :  0.01 (0.32), residues: 404

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   0.014   0.001   PHE B 326 
 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        0.00329 /  0.14 ( 5612)
  covalent geometry    : angle       0.49352 /  0.26 ( 7706)
  hydrogen bonds       : bond        0.03668 /  2.48 (  182)
  hydrogen bonds       : angle       4.30669 /  3.03 (  494)
  metal coordination   : bond        0.00625 /  0.37 (   16)
  metal coordination   : angle       2.54114 /  1.72 (   15)
  Misc. bond           : bond        0.00026 /  0.01 (    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
  114 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 106
  time to evaluate  : 0.129 
Fit side-chains
REVERT: A   65 GLN cc_start: 0.8701 (mt0) cc_final: 0.8429 (mt0)
REVERT: B  160 ASN cc_start: 0.8203 (p0) cc_final: 0.8000 (p0)
REVERT: B  328 VAL cc_start: 0.9009 (OUTLIER) cc_final: 0.8759 (t)
  outliers start: 8
  outliers final: 7
  residues processed: 107
  average time/residue: 0.4620
  time to fit residues: 51.4508
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  : 0.128 
-------------------------------------------------------------------------------
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  299 ILE
Chi-restraints excluded: chain B residue  328 VAL
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:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 17 optimal weight:    0.8980
   chunk 3 optimal weight:    0.0670
   chunk 61 optimal weight:    0.6980
   chunk 46 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   chunk 20 optimal weight:    0.8980
   overall best weight:    0.6518

-------------------------------------------------------------------------------
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 = 0.3669 r_free = 0.3669 target = 0.121240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.102987 restraints weight = 17977.048|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 2.59
r_work: 0.3275 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3280
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3280 r_free = 0.3280    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 = 0.3280 r_free = 0.3280    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: 0.3280
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.1717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5629  Z= 0.183
  Angle     :  0.528   7.217   7721  Z= 0.268
  Chirality :  0.043   0.149    859
  Planarity :  0.004   0.069    928
  Dihedral  : 10.473  73.420    962
  Min Nonbonded Distance : 1.923

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 15.11 %
    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:  0.16 (0.33), residues: 644
  helix:  0.97 (0.42), residues: 163
  sheet: -0.63 (0.58), residues: 77
  loop : -0.02 (0.32), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 476 
 TYR   0.011   0.002   TYR B 420 
 PHE   0.013   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        0.00447 /  0.18 ( 5612)
  covalent geometry    : angle       0.51395 /  0.27 ( 7706)
  hydrogen bonds       : bond        0.03954 /  2.68 (  182)
  hydrogen bonds       : angle       4.34859 /  3.04 (  494)
  metal coordination   : bond        0.00849 /  0.48 (   16)
  metal coordination   : angle       2.76226 /  1.87 (   15)
  Misc. bond           : bond        0.00031 /  0.02 (    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
  113 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 104
  time to evaluate  : 0.157 
Fit side-chains
REVERT: A   65 GLN cc_start: 0.8692 (mt0) cc_final: 0.8377 (mt0)
REVERT: B   47 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8720 (ptmm)
REVERT: B  160 ASN cc_start: 0.8207 (p0) cc_final: 0.7993 (p0)
REVERT: B  328 VAL cc_start: 0.8994 (OUTLIER) cc_final: 0.8752 (t)
  outliers start: 9
  outliers final: 5
  residues processed: 107
  average time/residue: 0.4520
  time to fit residues: 50.3653
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  : 0.111 
-------------------------------------------------------------------------------
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  328 VAL
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:    0.0670
   chunk 47 optimal weight:    0.7980
   chunk 24 optimal weight:    0.6980
   chunk 33 optimal weight:    0.3980
   chunk 25 optimal weight:    0.5980
   chunk 51 optimal weight:    0.7980
   chunk 7 optimal weight:    0.6980
   chunk 54 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.4918

-------------------------------------------------------------------------------
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 = 0.3672 r_free = 0.3672 target = 0.121506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.102875 restraints weight = 20632.565|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 2.79
r_work: 0.3265 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3270
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3270 r_free = 0.3270    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3270 r_free = 0.3270    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3270
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.1752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   5629  Z= 0.147
  Angle     :  0.513   6.995   7721  Z= 0.261
  Chirality :  0.042   0.148    859
  Planarity :  0.004   0.069    928
  Dihedral  : 10.476  73.402    962
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 15.11 %
    Favored  : 83.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.21 (0.33), residues: 644
  helix:  1.07 (0.42), residues: 163
  sheet: -0.64 (0.58), residues: 77
  loop : -0.01 (0.32), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 476 
 TYR   0.011   0.001   TYR B 420 
 PHE   0.014   0.001   PHE B 326 
 TRP   0.008   0.001   TRP B 159 
 HIS   0.004   0.001   HIS B 283 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00354 /  0.15 ( 5612)
  covalent geometry    : angle       0.49921 /  0.26 ( 7706)
  hydrogen bonds       : bond        0.03765 /  2.54 (  182)
  hydrogen bonds       : angle       4.30340 /  3.01 (  494)
  metal coordination   : bond        0.00642 /  0.38 (   16)
  metal coordination   : angle       2.68940 /  1.83 (   15)
  Misc. bond           : bond        0.00017 /  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
  113 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 105
  time to evaluate  : 0.197 
Fit side-chains
REVERT: A   65 GLN cc_start: 0.8691 (mt0) cc_final: 0.8368 (mt0)
REVERT: B   47 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8722 (ptmm)
REVERT: B  160 ASN cc_start: 0.8203 (p0) cc_final: 0.7992 (p0)
REVERT: B  328 VAL cc_start: 0.8994 (OUTLIER) cc_final: 0.8750 (t)
  outliers start: 8
  outliers final: 6
  residues processed: 106
  average time/residue: 0.4509
  time to fit residues: 49.8040
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  : 0.153 
-------------------------------------------------------------------------------
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  328 VAL
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:    0.0060
   chunk 26 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0570
   chunk 39 optimal weight:    0.4980
   chunk 19 optimal weight:    0.4980
   chunk 31 optimal weight:    0.9980
   chunk 44 optimal weight:    0.5980
   chunk 57 optimal weight:    0.0870
   chunk 16 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.2292

-------------------------------------------------------------------------------
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 = 0.3698 r_free = 0.3698 target = 0.125104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.107768 restraints weight = 12457.069|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 2.15
r_work: 0.3339 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3180 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3185
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3185 r_free = 0.3185    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3185 r_free = 0.3185    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3185
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8368
moved from start:          0.1794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   5629  Z= 0.100
  Angle     :  0.486   6.797   7721  Z= 0.248
  Chirality :  0.041   0.146    859
  Planarity :  0.004   0.073    928
  Dihedral  : 10.449  73.393    962
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 15.83 %
    Favored  : 82.91 %
  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 (0.34), residues: 644
  helix:  1.26 (0.42), residues: 162
  sheet: -0.53 (0.60), residues: 73
  loop :  0.01 (0.32), residues: 409

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   0.015   0.001   PHE B 326 
 TRP   0.009   0.001   TRP B 227 
 HIS   0.002   0.001   HIS B 427 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00230 /  0.10 ( 5612)
  covalent geometry    : angle       0.47608 /  0.25 ( 7706)
  hydrogen bonds       : bond        0.03439 /  2.32 (  182)
  hydrogen bonds       : angle       4.25107 /  3.01 (  494)
  metal coordination   : bond        0.00395 /  0.25 (   16)
  metal coordination   : angle       2.31051 /  1.58 (   15)
  Misc. bond           : bond        0.00009 /  0.00 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1967.77 seconds
wall clock time: 34 minutes 11.48 seconds (2051.48 seconds total)