Starting phenix.real_space_refine
on Sat May  2 13:01:56 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9yro_73372/05_2026/9yro_73372.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9yro_73372/05_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_73372/05_2026/9yro_73372.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9yro_73372/05_2026/9yro_73372.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9yro_73372/05_2026/9yro_73372.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9yro_73372/05_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-2.1rc2-6044/lib/python3.9/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: 2.17, per 1000 atoms: 0.40
  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: 0.54
  Conformation dependent library (CDL) restraints added in 470.7 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: 0.63
  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: 0.96

  Time building geometry restraints manager: 0.71 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:             2.250
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.280
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
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= 0.287
  Angle     :  0.973  60.818   7721  Z= 0.455
  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
  covalent geometry    : bond        0.00546 ( 5612)
  covalent geometry    : angle       0.96610 ( 7706)
  hydrogen bonds       : bond        0.14848 (  182)
  hydrogen bonds       : angle       6.31248 (  494)
  metal coordination   : bond        0.00597 (   16)
  metal coordination   : angle       2.80177 (   15)
  Misc. bond           : bond        0.04007 (    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  : 0.172 
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: 0.6600
  time to fit residues: 92.3952
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  : 0.204 
-------------------------------------------------------------------------------
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:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3674 r_free = 0.3674 target = 0.123372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.103540 restraints weight = 25123.007|
|-----------------------------------------------------------------------------|
r_work (start): 0.3413 rms_B_bonded: 3.22
r_work: 0.3225 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3225
-------------------------------------------------------------------------------
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 = 0.48   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 |
|-----------------------------------------------------------------------------|
r_final: 0.3228
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.1235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   5629  Z= 0.215
  Angle     :  0.582   6.678   7721  Z= 0.294
  Chirality :  0.045   0.153    859
  Planarity :  0.005   0.046    928
  Dihedral  : 11.890 122.926    962
  Min Nonbonded Distance : 1.914

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 12.05 %
    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: -0.16 (0.33), residues: 644
  helix:  0.22 (0.41), residues: 163
  sheet: -0.49 (0.57), residues: 77
  loop : -0.07 (0.32), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 476 
 TYR   0.012   0.002   TYR B 237 
 PHE   0.012   0.002   PHE A  16 
 TRP   0.011   0.001   TRP A 123 
 HIS   0.007   0.001   HIS B 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00518 ( 5612)
  covalent geometry    : angle       0.56804 ( 7706)
  hydrogen bonds       : bond        0.04545 (  182)
  hydrogen bonds       : angle       4.73172 (  494)
  metal coordination   : bond        0.00973 (   16)
  metal coordination   : angle       2.90664 (   15)
  Misc. bond           : bond        0.00015 (    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
  111 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 104
  time to evaluate  : 0.182 
Fit side-chains
REVERT: A   53 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8345 (mt0)
REVERT: B  241 MET cc_start: 0.8593 (ptp) cc_final: 0.8380 (ptp)
REVERT: B  328 VAL cc_start: 0.9050 (p) cc_final: 0.8835 (t)
REVERT: B  334 ASN cc_start: 0.8027 (t0) cc_final: 0.7769 (t160)
  outliers start: 7
  outliers final: 2
  residues processed: 105
  average time/residue: 0.6168
  time to fit residues: 67.1988
Evaluate side-chains
  103 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 100
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain A residue   53 GLN
Chi-restraints excluded: chain A residue  102 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 42 optimal weight:    0.0980
   chunk 11 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0980
   chunk 5 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 43 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 57 optimal weight:    0.0980
   chunk 16 optimal weight:    0.5980
   overall best weight:    0.2980

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3689 r_free = 0.3689 target = 0.122741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.103386 restraints weight = 24889.191|
|-----------------------------------------------------------------------------|
r_work (start): 0.3441 rms_B_bonded: 3.15
r_work: 0.3259 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3262
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3262 r_free = 0.3262    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3262 r_free = 0.3262    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3262
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.1425

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= 0.112
  Angle     :  0.499   5.673   7721  Z= 0.254
  Chirality :  0.041   0.148    859
  Planarity :  0.004   0.053    928
  Dihedral  : 10.854  88.008    962
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 3.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 14.57 %
    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:  0.10 (0.33), residues: 644
  helix:  0.66 (0.42), residues: 163
  sheet: -0.40 (0.57), residues: 83
  loop :  0.02 (0.32), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 476 
 TYR   0.010   0.001   TYR B 420 
 PHE   0.008   0.001   PHE B 426 
 TRP   0.008   0.001   TRP B 385 
 HIS   0.003   0.001   HIS B 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 5612)
  covalent geometry    : angle       0.48874 ( 7706)
  hydrogen bonds       : bond        0.03625 (  182)
  hydrogen bonds       : angle       4.43756 (  494)
  metal coordination   : bond        0.00444 (   16)
  metal coordination   : angle       2.32154 (   15)
  Misc. bond           : bond        0.00013 (    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: 8
    poor density    : 108
  time to evaluate  : 0.200 
Fit side-chains
REVERT: A   65 GLN cc_start: 0.8676 (mt0) cc_final: 0.8388 (mt0)
REVERT: B   47 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8753 (pttp)
REVERT: B  144 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7920 (m-30)
REVERT: B  328 VAL cc_start: 0.9033 (p) cc_final: 0.8795 (t)
REVERT: B  334 ASN cc_start: 0.7961 (t0) cc_final: 0.7649 (t160)
  outliers start: 8
  outliers final: 3
  residues processed: 110
  average time/residue: 0.5930
  time to fit residues: 67.7943
Evaluate side-chains
  110 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 105
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
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  144 ASP
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:    0.9990
   chunk 0 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 22 optimal weight:    3.9990
   chunk 61 optimal weight:    0.2980
   chunk 42 optimal weight:    0.0670
   chunk 34 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0170
   chunk 50 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 62 optimal weight:    0.5980
   overall best weight:    0.3356

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

Flipped N/Q/H residues before XYZ refinement:
B 254 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.122847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.104390 restraints weight = 19578.773|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 2.74
r_work: 0.3287 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3277
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3277 r_free = 0.3277    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 = 0.3277 r_free = 0.3277    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3277
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.1573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5629  Z= 0.118
  Angle     :  0.497   5.591   7721  Z= 0.255
  Chirality :  0.041   0.148    859
  Planarity :  0.004   0.049    928
  Dihedral  : 10.552  73.300    962
  Min Nonbonded Distance : 1.966

Molprobity Statistics.
  All-atom Clashscore : 2.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 13.85 %
    Favored  : 84.53 %
  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:  0.93 (0.42), residues: 163
  sheet: -0.42 (0.57), residues: 84
  loop :  0.06 (0.32), residues: 397

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   0.010   0.001   PHE A  68 
 TRP   0.007   0.001   TRP B 385 
 HIS   0.004   0.001   HIS B 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 5612)
  covalent geometry    : angle       0.48645 ( 7706)
  hydrogen bonds       : bond        0.03487 (  182)
  hydrogen bonds       : angle       4.34573 (  494)
  metal coordination   : bond        0.00564 (   16)
  metal coordination   : angle       2.34647 (   15)
  Misc. bond           : bond        0.00033 (    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
  113 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 104
  time to evaluate  : 0.224 
Fit side-chains
REVERT: A   65 GLN cc_start: 0.8659 (mt0) cc_final: 0.8363 (mt0)
REVERT: B   47 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8751 (pttp)
REVERT: B   57 MET cc_start: 0.8587 (mmp) cc_final: 0.7701 (mmt)
REVERT: B  144 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7839 (m-30)
REVERT: B  328 VAL cc_start: 0.9011 (p) cc_final: 0.8766 (t)
  outliers start: 9
  outliers final: 3
  residues processed: 109
  average time/residue: 0.6284
  time to fit residues: 71.1925
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  : 0.168 
-------------------------------------------------------------------------------
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  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:    0.9990
   chunk 20 optimal weight:    0.0980
   chunk 29 optimal weight:    0.4980
   chunk 62 optimal weight:    0.2980
   chunk 3 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   chunk 21 optimal weight:    0.4980
   chunk 32 optimal weight:    0.2980
   chunk 51 optimal weight:    0.9990
   chunk 52 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.3380

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

Flipped N/Q/H residues before XYZ refinement:
B  95 HIS
B 148 HIS
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 = 0.122696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.104601 restraints weight = 16805.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.3458 rms_B_bonded: 2.53
r_work: 0.3308 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3311
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3311 r_free = 0.3311    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3311 r_free = 0.3311    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3311
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.1687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5629  Z= 0.117
  Angle     :  0.491   5.620   7721  Z= 0.250
  Chirality :  0.041   0.149    859
  Planarity :  0.004   0.050    928
  Dihedral  : 10.482  73.305    962
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 14.39 %
    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:  0.31 (0.34), residues: 644
  helix:  1.07 (0.42), residues: 163
  sheet: -0.55 (0.56), residues: 84
  loop :  0.11 (0.32), residues: 397

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   0.009   0.001   PHE A  68 
 TRP   0.006   0.001   TRP B 159 
 HIS   0.004   0.001   HIS B 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 5612)
  covalent geometry    : angle       0.48067 ( 7706)
  hydrogen bonds       : bond        0.03455 (  182)
  hydrogen bonds       : angle       4.28778 (  494)
  metal coordination   : bond        0.00539 (   16)
  metal coordination   : angle       2.32110 (   15)
  Misc. bond           : bond        0.00032 (    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  : 0.216 
Fit side-chains
REVERT: B   47 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8694 (pttm)
REVERT: B  144 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7817 (m-30)
REVERT: B  328 VAL cc_start: 0.8984 (p) cc_final: 0.8750 (t)
  outliers start: 10
  outliers final: 3
  residues processed: 107
  average time/residue: 0.6406
  time to fit residues: 71.2988
Evaluate side-chains
  106 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 101
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
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  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:    0.8980
   chunk 21 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 3 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9990
   chunk 7 optimal weight:    0.2980
   chunk 58 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B 108 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.121363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.102256 restraints weight = 22466.404|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 2.97
r_work: 0.3251 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3252
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3252 r_free = 0.3252    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 = 0.3252 r_free = 0.3252    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3252
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
moved from start:          0.1747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   5629  Z= 0.184
  Angle     :  0.536   6.228   7721  Z= 0.271
  Chirality :  0.043   0.151    859
  Planarity :  0.004   0.052    928
  Dihedral  : 10.485  73.349    962
  Min Nonbonded Distance : 1.921

Molprobity Statistics.
  All-atom Clashscore : 3.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  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:  0.22 (0.33), residues: 644
  helix:  1.01 (0.42), residues: 163
  sheet: -0.54 (0.57), residues: 77
  loop :  0.01 (0.32), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B 476 
 TYR   0.013   0.002   TYR B  51 
 PHE   0.011   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
  covalent geometry    : bond        0.00450 ( 5612)
  covalent geometry    : angle       0.52269 ( 7706)
  hydrogen bonds       : bond        0.03893 (  182)
  hydrogen bonds       : angle       4.38681 (  494)
  metal coordination   : bond        0.00869 (   16)
  metal coordination   : angle       2.73113 (   15)
  Misc. bond           : bond        0.00040 (    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: B  328 VAL cc_start: 0.9004 (p) cc_final: 0.8757 (t)
  outliers start: 7
  outliers final: 3
  residues processed: 106
  average time/residue: 0.6435
  time to fit residues: 70.8226
Evaluate side-chains
  103 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 100
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
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  513 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9980
   chunk 7 optimal weight:    0.5980
   chunk 1 optimal weight:    0.0980
   chunk 59 optimal weight:    0.7980
   chunk 49 optimal weight:    0.1980
   chunk 32 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 58 optimal weight:    0.1980
   chunk 33 optimal weight:    0.3980
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.2980

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

Flipped N/Q/H residues before XYZ refinement:
A  80 HIS
B 245 GLN
B 246 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.125433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.106931 restraints weight = 16469.325|
|-----------------------------------------------------------------------------|
r_work (start): 0.3456 rms_B_bonded: 2.57
r_work: 0.3302 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3291
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3291 r_free = 0.3291    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 = 0.3291 r_free = 0.3291    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3291
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.1866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5629  Z= 0.112
  Angle     :  0.504   8.187   7721  Z= 0.253
  Chirality :  0.041   0.150    859
  Planarity :  0.004   0.052    928
  Dihedral  : 10.456  73.356    962
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 16.01 %
    Favored  : 83.09 %
  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:  1.17 (0.42), residues: 163
  sheet: -0.49 (0.58), residues: 79
  loop :  0.05 (0.32), residues: 402

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   0.010   0.001   PHE A  68 
 TRP   0.008   0.001   TRP B 227 
 HIS   0.003   0.001   HIS B 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 5612)
  covalent geometry    : angle       0.49379 ( 7706)
  hydrogen bonds       : bond        0.03423 (  182)
  hydrogen bonds       : angle       4.21141 (  494)
  metal coordination   : bond        0.00470 (   16)
  metal coordination   : angle       2.32423 (   15)
  Misc. bond           : bond        0.00010 (    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
  107 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 102
  time to evaluate  : 0.209 
Fit side-chains
REVERT: B  328 VAL cc_start: 0.8984 (p) cc_final: 0.8739 (t)
  outliers start: 5
  outliers final: 5
  residues processed: 103
  average time/residue: 0.6241
  time to fit residues: 66.8901
Evaluate side-chains
  108 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 103
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
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  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:    0.0060
   chunk 35 optimal weight:    0.5980
   chunk 11 optimal weight:    0.5980
   chunk 26 optimal weight:    0.6980
   chunk 3 optimal weight:    0.0270
   chunk 47 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9990
   chunk 18 optimal weight:    0.8980
   chunk 44 optimal weight:    0.6980
   chunk 53 optimal weight:    3.9990
   overall best weight:    0.3854

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

Flipped N/Q/H residues before XYZ refinement:
B 245 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.122337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.103243 restraints weight = 23145.789|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 3.02
r_work: 0.3263 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3252
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3252 r_free = 0.3252    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 = 0.3252 r_free = 0.3252    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3252
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.1857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5629  Z= 0.126
  Angle     :  0.501   6.241   7721  Z= 0.253
  Chirality :  0.041   0.148    859
  Planarity :  0.004   0.057    928
  Dihedral  : 10.434  73.365    962
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  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:  0.39 (0.33), residues: 644
  helix:  1.22 (0.42), residues: 163
  sheet: -0.49 (0.59), residues: 73
  loop :  0.09 (0.32), residues: 408

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   0.010   0.001   TRP B 520 
 HIS   0.004   0.001   HIS B 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 5612)
  covalent geometry    : angle       0.49007 ( 7706)
  hydrogen bonds       : bond        0.03459 (  182)
  hydrogen bonds       : angle       4.17482 (  494)
  metal coordination   : bond        0.00581 (   16)
  metal coordination   : angle       2.41742 (   15)
  Misc. bond           : bond        0.00012 (    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
  109 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 102
  time to evaluate  : 0.195 
Fit side-chains
REVERT: B  328 VAL cc_start: 0.9015 (p) cc_final: 0.8755 (t)
  outliers start: 7
  outliers final: 4
  residues processed: 105
  average time/residue: 0.6402
  time to fit residues: 69.8808
Evaluate side-chains
  107 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 103
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 THR
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  144 ASP
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:    0.0070
   chunk 9 optimal weight:    0.9980
   chunk 53 optimal weight:    0.0570
   chunk 39 optimal weight:    0.6980
   chunk 17 optimal weight:    0.8980
   chunk 3 optimal weight:    0.0010
   chunk 61 optimal weight:    0.6980
   chunk 46 optimal weight:    0.0670
   chunk 10 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.1660

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

Flipped N/Q/H residues before XYZ refinement:
B 245 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 = 0.3718 r_free = 0.3718 target = 0.126638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.108020 restraints weight = 17488.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.3464 rms_B_bonded: 2.65
r_work: 0.3312 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3305
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3305 r_free = 0.3305    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3305 r_free = 0.3305    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3305
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.2006

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= 0.088
  Angle     :  0.474   6.098   7721  Z= 0.241
  Chirality :  0.040   0.146    859
  Planarity :  0.004   0.055    928
  Dihedral  : 10.394  73.379    962
  Min Nonbonded Distance : 1.999

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 16.01 %
    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:  0.52 (0.34), residues: 644
  helix:  1.58 (0.42), residues: 157
  sheet: -0.66 (0.57), residues: 75
  loop :  0.13 (0.32), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 476 
 TYR   0.009   0.001   TYR B 420 
 PHE   0.011   0.001   PHE B 326 
 TRP   0.009   0.001   TRP B 227 
 HIS   0.003   0.001   HIS B 148 

Details of bonding type rmsd
  covalent geometry    : bond        0.00198 ( 5612)
  covalent geometry    : angle       0.46663 ( 7706)
  hydrogen bonds       : bond        0.03106 (  182)
  hydrogen bonds       : angle       4.05918 (  494)
  metal coordination   : bond        0.00317 (   16)
  metal coordination   : angle       1.95495 (   15)
  Misc. bond           : bond        0.00005 (    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
  115 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 109
  time to evaluate  : 0.238 
Fit side-chains
REVERT: B   45 ILE cc_start: 0.8707 (mt) cc_final: 0.8385 (mt)
REVERT: B   47 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8680 (pttp)
REVERT: B  328 VAL cc_start: 0.8966 (p) cc_final: 0.8730 (t)
  outliers start: 6
  outliers final: 2
  residues processed: 112
  average time/residue: 0.5925
  time to fit residues: 69.0082
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  : 0.164 
-------------------------------------------------------------------------------
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  513 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 50 optimal weight:    0.0970
   chunk 47 optimal weight:    0.4980
   chunk 24 optimal weight:    0.0770
   chunk 33 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0770
   chunk 51 optimal weight:    0.5980
   chunk 7 optimal weight:    0.6980
   chunk 54 optimal weight:    0.0370
   chunk 61 optimal weight:    0.6980
   chunk 12 optimal weight:    0.8980
   chunk 29 optimal weight:    0.5980
   overall best weight:    0.1572

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

Flipped N/Q/H residues before XYZ refinement:
B  65 GLN
B 246 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.126770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.107384 restraints weight = 21603.214|
|-----------------------------------------------------------------------------|
r_work (start): 0.3464 rms_B_bonded: 2.99
r_work: 0.3293 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3282
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3282 r_free = 0.3282    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3282 r_free = 0.3282    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3282
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.2131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   5629  Z= 0.092
  Angle     :  0.484   5.761   7721  Z= 0.247
  Chirality :  0.040   0.144    859
  Planarity :  0.004   0.061    928
  Dihedral  : 10.372  73.400    962
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 16.73 %
    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:  0.56 (0.34), residues: 644
  helix:  1.66 (0.42), residues: 157
  sheet: -0.58 (0.58), residues: 73
  loop :  0.12 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 476 
 TYR   0.009   0.001   TYR B 420 
 PHE   0.013   0.001   PHE B 326 
 TRP   0.008   0.001   TRP B 520 
 HIS   0.002   0.001   HIS B 148 

Details of bonding type rmsd
  covalent geometry    : bond        0.00212 ( 5612)
  covalent geometry    : angle       0.47778 ( 7706)
  hydrogen bonds       : bond        0.03105 (  182)
  hydrogen bonds       : angle       3.94360 (  494)
  metal coordination   : bond        0.00297 (   16)
  metal coordination   : angle       1.86686 (   15)
  Misc. bond           : bond        0.00000 (    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: 4
    poor density    : 107
  time to evaluate  : 0.160 
Fit side-chains
REVERT: B   47 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8718 (ptmm)
REVERT: B  328 VAL cc_start: 0.8979 (p) cc_final: 0.8729 (t)
  outliers start: 4
  outliers final: 2
  residues processed: 109
  average time/residue: 0.6353
  time to fit residues: 71.9995
Evaluate side-chains
  108 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 105
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
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  513 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 45 optimal weight:    0.0970
   chunk 26 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0070
   chunk 31 optimal weight:    0.0470
   chunk 44 optimal weight:    0.5980
   chunk 57 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.3494

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

Flipped N/Q/H residues before XYZ refinement:
B 246 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.123222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.106183 restraints weight = 12498.812|
|-----------------------------------------------------------------------------|
r_work (start): 0.3476 rms_B_bonded: 2.10
r_work: 0.3346 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3190 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3184
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3184 r_free = 0.3184    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3184 r_free = 0.3184    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3184
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.2126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5629  Z= 0.120
  Angle     :  0.493   5.800   7721  Z= 0.252
  Chirality :  0.041   0.145    859
  Planarity :  0.004   0.058    928
  Dihedral  : 10.369  73.391    962
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 17.09 %
    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:  0.49 (0.33), residues: 644
  helix:  1.65 (0.42), residues: 157
  sheet: -0.89 (0.53), residues: 82
  loop :  0.15 (0.32), residues: 405

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   0.033   0.001   PHE B 326 
 TRP   0.009   0.001   TRP B 520 
 HIS   0.003   0.001   HIS B 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 5612)
  covalent geometry    : angle       0.48370 ( 7706)
  hydrogen bonds       : bond        0.03352 (  182)
  hydrogen bonds       : angle       4.00549 (  494)
  metal coordination   : bond        0.00531 (   16)
  metal coordination   : angle       2.18859 (   15)
  Misc. bond           : bond        0.00012 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2566.99 seconds
wall clock time: 44 minutes 30.60 seconds (2670.60 seconds total)