Starting phenix.real_space_refine
on Sat Oct 11 21:21:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pt7_17869/10_2025/8pt7_17869.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pt7_17869/10_2025/8pt7_17869.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pt7_17869/10_2025/8pt7_17869.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pt7_17869/10_2025/8pt7_17869.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pt7_17869/10_2025/8pt7_17869.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pt7_17869/10_2025/8pt7_17869.cif"
  }
  resolution = 2.8
  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=   0.000 sd=   0.002
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      1      6.06       5
     P      29      5.49       5
     Mg      1      5.21       5
     S      51      5.16       5
     C    5565      2.51       5
     N    1601      2.21       5
     O    1784      1.98       5
     H    8690      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 17722
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 6652
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 417, 6652
          Classifications: {'peptide': 417}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 22, 'TRANS': 394}
    Chain: "B"
      Number of atoms: 7973
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 515, 7973
          Classifications: {'peptide': 515}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 493}
    Chain: "C"
      Number of atoms: 2221
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2221
          Classifications: {'peptide': 139}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 133}
    Chain: "V"
      Number of atoms: 408
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 408
          Classifications: {'RNA': 14}
          Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 4, 'rna3p_pyr': 6}
          Link IDs: {'rna2p': 4, 'rna3p': 9}
    Chain: "S"
      Number of atoms: 466
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 466
          Classifications: {'RNA': 15}
          Modifications used: {'3*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 6, 'rna3p_pyr': 3}
          Link IDs: {'rna2p': 6, 'rna3p': 8}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2583  SG  CYS A 161      46.948  44.799 105.483  1.00 56.25           S
  ATOM   4472  SG  CYS A 282      45.858  47.622 107.959  1.00 69.01           S

  Time building chain proxies: 3.45, per 1000 atoms: 0.19
  Number of scatterers: 17722
  At special positions: 0
  Unit cell: (87.36, 95.76, 124.32, 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      1     29.99
     S      51     16.00
     P      29     15.00
     Mg      1     11.99
     O    1784      8.00
     N    1601      7.00
     C    5565      6.00
     H    8690      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.60
  Conformation dependent library (CDL) restraints added in 496.2 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 501 "
        pdb="ZN    ZN A 501 " - pdb=" ND1 HIS A 284 "
        pdb="ZN    ZN A 501 " - pdb=" NE2 HIS A 296 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 282 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 161 "
      Number of angles added : 2


  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2020

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 10 sheets defined
      45.5% alpha, 13.4% beta
      7 base pairs and 8 stacking pairs defined.
    Time for finding SS restraints: 3.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 13
      removed outlier: 3.700A  pdb=" N   CYS A  13 " --> pdb=" O   THR A   9 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 94
    Processing helix  chain 'A' and resid 112 through 123
    Processing helix  chain 'A' and resid 141 through 157
      removed outlier: 3.575A  pdb=" N   ILE A 145 " --> pdb=" O   ARG A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 169
    Processing helix  chain 'A' and resid 174 through 189
    Processing helix  chain 'A' and resid 223 through 237
    Processing helix  chain 'A' and resid 301 through 310
    Processing helix  chain 'A' and resid 312 through 323
      removed outlier: 4.481A  pdb=" N   ASP A 323 " --> pdb=" O   ILE A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 344 through 356
      removed outlier: 3.539A  pdb=" N   VAL A 348 " --> pdb=" O   THR A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 374
      removed outlier: 3.859A  pdb=" N   ALA A 363 " --> pdb=" O   ARG A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 387
    Processing helix  chain 'A' and resid 388 through 392
    Processing helix  chain 'A' and resid 394 through 415
    Processing helix  chain 'B' and resid 1 through 5
      removed outlier: 3.780A  pdb=" N   GLN B   5 " --> pdb=" O   TRP B   2 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 23 through 40
    Processing helix  chain 'B' and resid 65 through 70
      removed outlier: 3.896A  pdb=" N   LEU B  69 " --> pdb=" O   VAL B  65 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 92 through 104
    Processing helix  chain 'B' and resid 107 through 117
    Processing helix  chain 'B' and resid 130 through 137
    Processing helix  chain 'B' and resid 161 through 183
      removed outlier: 3.729A  pdb=" N   VAL B 170 " --> pdb=" O   LEU B 166 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 184 through 187
      removed outlier: 3.763A  pdb=" N   THR B 187 " --> pdb=" O   ALA B 184 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 184 through 187'
    Processing helix  chain 'B' and resid 191 through 203
    Processing helix  chain 'B' and resid 222 through 234
    Processing helix  chain 'B' and resid 235 through 248
      removed outlier: 3.720A  pdb=" N   GLY B 239 " --> pdb=" O   MET B 235 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   VAL B 240 " --> pdb=" O   GLY B 236 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 279
    Processing helix  chain 'B' and resid 297 through 311
    Processing helix  chain 'B' and resid 354 through 372
      removed outlier: 3.965A  pdb=" N   LEU B 359 " --> pdb=" O   PRO B 355 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 376 through 396
    Processing helix  chain 'B' and resid 409 through 413
      removed outlier: 3.692A  pdb=" N   GLY B 413 " --> pdb=" O   THR B 410 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 419 through 425
    Processing helix  chain 'B' and resid 429 through 436
      removed outlier: 3.944A  pdb=" N   GLN B 434 " --> pdb=" O   PHE B 431 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 442 through 454
    Processing helix  chain 'B' and resid 479 through 498
    Processing helix  chain 'B' and resid 506 through 514
    Processing helix  chain 'C' and resid 3 through 8
    Processing helix  chain 'C' and resid 16 through 23
    Processing helix  chain 'C' and resid 34 through 40
    Processing helix  chain 'C' and resid 42 through 55
    Processing helix  chain 'C' and resid 56 through 59
    Processing helix  chain 'C' and resid 87 through 97
    Processing helix  chain 'C' and resid 100 through 109
      removed outlier: 3.996A  pdb=" N   GLN C 109 " --> pdb=" O   SER C 105 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 27
      removed outlier: 3.571A  pdb=" N   TYR A  45 " --> pdb=" O   LEU A  26 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   TRP A  52 " --> pdb=" O   VAL A  69 " (cutoff:3.500A)
      removed outlier: 7.656A  pdb=" N   CYS A  71 " --> pdb=" O   TRP A  52 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   ALA A  54 " --> pdb=" O   CYS A  71 " (cutoff:3.500A)
      removed outlier: 7.791A  pdb=" N   LEU A  73 " --> pdb=" O   ALA A  54 " (cutoff:3.500A)
      removed outlier: 7.454A  pdb=" N   GLU A  56 " --> pdb=" O   LEU A  73 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   THR A  78 " --> pdb=" O   ASN A  74 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 136 through 137
    Processing sheet with id=AA3, first strand: chain 'A' and resid 192 through 194
      removed outlier: 7.449A  pdb=" N   TRP A 198 " --> pdb=" O   PRO A 253 " (cutoff:3.500A)
      removed outlier: 8.228A  pdb=" N   MET A 255 " --> pdb=" O   TRP A 198 " (cutoff:3.500A)
      removed outlier: 6.049A  pdb=" N   GLN A 200 " --> pdb=" O   MET A 255 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 192 through 194
      removed outlier: 7.449A  pdb=" N   TRP A 198 " --> pdb=" O   PRO A 253 " (cutoff:3.500A)
      removed outlier: 8.228A  pdb=" N   MET A 255 " --> pdb=" O   TRP A 198 " (cutoff:3.500A)
      removed outlier: 6.049A  pdb=" N   GLN A 200 " --> pdb=" O   MET A 255 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   SER A 248 " --> pdb=" O   LEU A 277 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   LEU A 277 " --> pdb=" O   SER A 248 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 74 through 80
    Processing sheet with id=AA6, first strand: chain 'B' and resid 124 through 125
    Processing sheet with id=AA7, first strand: chain 'B' and resid 155 through 159
      removed outlier: 3.879A  pdb=" N   ARG B 155 " --> pdb=" O   ARG B 145 " (cutoff:3.500A)
      removed outlier: 7.221A  pdb=" N   PHE B 140 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 327 through 329
    Processing sheet with id=AA9, first strand: chain 'B' and resid 477 through 478
    Processing sheet with id=AB1, first strand: chain 'C' and resid 71 through 83
      removed outlier: 9.430A  pdb=" N   LYS C  73 " --> pdb=" O   SER C 121 " (cutoff:3.500A)
      removed outlier: 8.410A  pdb=" N   SER C 121 " --> pdb=" O   LYS C  73 " (cutoff:3.500A)
      removed outlier: 7.375A  pdb=" N   LYS C  75 " --> pdb=" O   TYR C 119 " (cutoff:3.500A)
      removed outlier: 5.318A  pdb=" N   TYR C 119 " --> pdb=" O   LYS C  75 " (cutoff:3.500A)

    395 hydrogen bonds defined for protein.
    1086 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      16 hydrogen bonds
      28 hydrogen bond angles
      0 basepair planarities
      7 basepair parallelities
      8 stacking parallelities
  Total time for adding SS restraints: 4.42

  Time building geometry restraints manager: 2.19 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 8662
        1.03 -     1.23: 37
        1.23 -     1.42: 3911
        1.42 -     1.62: 5276
        1.62 -     1.81: 72
  Bond restraints: 17958
  Sorted by residual:
  bond pdb=" C   LEU C  56 "
       pdb=" N   PRO C  57 "
    ideal  model  delta    sigma   weight residual
    1.334  1.354 -0.020 2.34e-02 1.83e+03 7.35e-01
  bond pdb=" CG  PRO C  57 "
       pdb=" CD  PRO C  57 "
    ideal  model  delta    sigma   weight residual
    1.503  1.479  0.024 3.40e-02 8.65e+02 5.08e-01
  bond pdb=" CB  ASP B 467 "
       pdb=" CG  ASP B 467 "
    ideal  model  delta    sigma   weight residual
    1.516  1.534 -0.018 2.50e-02 1.60e+03 4.98e-01
  bond pdb=" CA  PRO C  57 "
       pdb=" C   PRO C  57 "
    ideal  model  delta    sigma   weight residual
    1.520  1.529 -0.009 1.42e-02 4.96e+03 4.28e-01
  bond pdb=" N   GLY B 262 "
       pdb=" CA  GLY B 262 "
    ideal  model  delta    sigma   weight residual
    1.444  1.451 -0.007 1.06e-02 8.90e+03 3.77e-01
  ... (remaining 17953 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.85: 29208
        0.85 -     1.70: 2945
        1.70 -     2.55: 164
        2.55 -     3.41: 74
        3.41 -     4.26: 12
  Bond angle restraints: 32403
  Sorted by residual:
  angle pdb=" CA  GLU C  89 "
        pdb=" CB  GLU C  89 "
        pdb=" CG  GLU C  89 "
      ideal   model   delta    sigma   weight residual
     114.10  117.48   -3.38 2.00e+00 2.50e-01 2.85e+00
  angle pdb=" N   ASP B 467 "
        pdb=" CA  ASP B 467 "
        pdb=" C   ASP B 467 "
      ideal   model   delta    sigma   weight residual
     110.91  108.97    1.94 1.17e+00 7.31e-01 2.74e+00
  angle pdb=" C   ASP C 110 "
        pdb=" N   ARG C 111 "
        pdb=" CA  ARG C 111 "
      ideal   model   delta    sigma   weight residual
     122.21  119.64    2.57 1.62e+00 3.81e-01 2.52e+00
  angle pdb=" N   VAL A 414 "
        pdb=" CA  VAL A 414 "
        pdb=" C   VAL A 414 "
      ideal   model   delta    sigma   weight residual
     111.81  110.47    1.34 8.60e-01 1.35e+00 2.45e+00
  angle pdb=" C   ASP A 301 "
        pdb=" CA  ASP A 301 "
        pdb=" CB  ASP A 301 "
      ideal   model   delta    sigma   weight residual
     109.45  112.21   -2.76 1.81e+00 3.05e-01 2.33e+00
  ... (remaining 32398 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 7435
       17.86 -    35.72: 695
       35.72 -    53.58: 251
       53.58 -    71.45: 74
       71.45 -    89.31: 22
  Dihedral angle restraints: 8477
    sinusoidal: 4872
      harmonic: 3605
  Sorted by residual:
  dihedral pdb=" CA  LEU B 265 "
           pdb=" C   LEU B 265 "
           pdb=" N   MET B 266 "
           pdb=" CA  MET B 266 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.00   19.00     0      5.00e+00 4.00e-02 1.44e+01
  dihedral pdb=" CB  GLU A 326 "
           pdb=" CG  GLU A 326 "
           pdb=" CD  GLU A 326 "
           pdb=" OE1 GLU A 326 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.31  -89.31     1      3.00e+01 1.11e-03 1.05e+01
  dihedral pdb=" CB  GLU A 381 "
           pdb=" CG  GLU A 381 "
           pdb=" CD  GLU A 381 "
           pdb=" OE1 GLU A 381 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.27   89.27     1      3.00e+01 1.11e-03 1.05e+01
  ... (remaining 8474 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 918
       0.026 -    0.053: 376
       0.053 -    0.079: 76
       0.079 -    0.105: 44
       0.105 -    0.132: 31
  Chirality restraints: 1445
  Sorted by residual:
  chirality pdb=" CA  VAL C 112 "
            pdb=" N   VAL C 112 "
            pdb=" C   VAL C 112 "
            pdb=" CB  VAL C 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.33e-01
  chirality pdb=" CA  ILE B 125 "
            pdb=" N   ILE B 125 "
            pdb=" C   ILE B 125 "
            pdb=" CB  ILE B 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.15e-01
  chirality pdb=" CA  ILE B 253 "
            pdb=" N   ILE B 253 "
            pdb=" C   ILE B 253 "
            pdb=" CB  ILE B 253 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.10e-01
  ... (remaining 1442 not shown)

  Planarity restraints: 2560
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 469 "    0.032 5.00e-02 4.00e+02   4.91e-02 3.85e+00
        pdb=" N   PRO B 470 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO B 470 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 470 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 133 "    0.126 9.50e-02 1.11e+02   4.21e-02 2.13e+00
        pdb=" NE  ARG A 133 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 133 "    0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 133 "    0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 133 "   -0.000 2.00e-02 2.50e+03
        pdb="HH11 ARG A 133 "   -0.004 2.00e-02 2.50e+03
        pdb="HH12 ARG A 133 "   -0.000 2.00e-02 2.50e+03
        pdb="HH21 ARG A 133 "    0.001 2.00e-02 2.50e+03
        pdb="HH22 ARG A 133 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A V   4 "   -0.020 2.00e-02 2.50e+03   8.07e-03 2.12e+00
        pdb=" N9    A V   4 "    0.019 2.00e-02 2.50e+03
        pdb=" C8    A V   4 "    0.001 2.00e-02 2.50e+03
        pdb=" N7    A V   4 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    A V   4 "    0.000 2.00e-02 2.50e+03
        pdb=" C6    A V   4 "   -0.002 2.00e-02 2.50e+03
        pdb=" N6    A V   4 "   -0.005 2.00e-02 2.50e+03
        pdb=" N1    A V   4 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2    A V   4 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    A V   4 "    0.002 2.00e-02 2.50e+03
        pdb=" C4    A V   4 "    0.004 2.00e-02 2.50e+03
        pdb=" H8    A V   4 "    0.001 2.00e-02 2.50e+03
        pdb=" H2    A V   4 "    0.001 2.00e-02 2.50e+03
  ... (remaining 2557 not shown)

  Histogram of nonbonded interaction distances:
        1.57 -     2.18: 831
        2.18 -     2.78: 34123
        2.78 -     3.39: 49388
        3.39 -     3.99: 65796
        3.99 -     4.60: 101554
  Nonbonded interactions: 251692
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN B  57 "
            pdb=" HZ1 LYS B 181 "
     model   vdw
     1.569 2.450
  nonbonded pdb=" OE1 GLU C  89 "
            pdb=" H   GLU C  89 "
     model   vdw
     1.570 2.450
  nonbonded pdb=" O2    C V  13 "
            pdb=" H21   G S   3 "
     model   vdw
     1.609 2.450
  nonbonded pdb=" O   PRO B  17 "
            pdb=" H   GLN B 147 "
     model   vdw
     1.627 2.450
  nonbonded pdb=" O   ASN B 330 "
            pdb=" HG  SER B 331 "
     model   vdw
     1.646 2.450
  ... (remaining 251687 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.130
  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:             0.100
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     24.290
  Find NCS groups from input model:        0.060
  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:             0.010
  Load rotamer database and sin/cos tables:8.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8898
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      :  0.002   0.024   9272  Z= 0.096
  Angle     :  0.437   4.257  12662  Z= 0.232
  Chirality :  0.035   0.132   1445
  Planarity :  0.003   0.055   1525
  Dihedral  : 18.022  89.308   3653
  Min Nonbonded Distance : 1.778

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.44 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 23.44 %
    Favored  : 75.27 %
  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 aren not related in a simple way.
  whole:  1.49 (0.26), residues: 1065
  helix:  1.94 (0.25), residues: 462
  sheet:  0.75 (0.52), residues: 87
  loop :  0.23 (0.28), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 133 
 TYR   0.011   0.001   TYR C  95 
 PHE   0.006   0.001   PHE C  44 
 TRP   0.004   0.001   TRP A 136 
 HIS   0.002   0.001   HIS A 371 

Details of bonding type rmsd
  covalent geometry    : bond        0.00211 ( 9268)
  covalent geometry    : angle       0.43610 (12660)
  hydrogen bonds       : bond        0.13682 (  407)
  hydrogen bonds       : angle       5.52501 ( 1114)
  metal coordination   : bond        0.00310 (    4)
  metal coordination   : angle       1.76563 (    2)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 0.480 
Fit side-chains
   revert: symmetry clash
REVERT: B   38 MET cc_start: 0.9239 (tpt) cc_final: 0.8756 (tpt)
  outliers start: 12
  outliers final: 8
  residues processed: 100
  average time/residue: 1.3551
  time to fit residues: 144.2858
Evaluate side-chains
  95 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 87
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain B residue   59 GLU
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue   75 CYS
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  444 ASP
Chi-restraints excluded: chain C residue   67 SER
Chi-restraints excluded: chain C residue  125 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 100 optimal weight:    3.9990
   chunk 106 optimal weight:    5.9990
   chunk 38 optimal weight:    1.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN
A 195 ASN
B 491 GLN
C 109 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.112286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.076746 restraints weight = 34707.054|
|-----------------------------------------------------------------------------|
r_work (start): 0.2829 rms_B_bonded: 1.95
r_work: 0.2702 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2575 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8933
moved from start:          0.0645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9272  Z= 0.151
  Angle     :  0.471   4.219  12662  Z= 0.248
  Chirality :  0.037   0.171   1445
  Planarity :  0.004   0.049   1525
  Dihedral  : 11.439  73.673   1613
  Min Nonbonded Distance : 1.832

Molprobity Statistics.
  All-atom Clashscore : 1.63
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.54 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 21.83 %
    Favored  : 76.34 %
  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 aren not related in a simple way.
  whole:  1.41 (0.26), residues: 1065
  helix:  1.88 (0.25), residues: 465
  sheet:  0.84 (0.54), residues: 85
  loop :  0.15 (0.27), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 133 
 TYR   0.013   0.001   TYR A 403 
 PHE   0.011   0.001   PHE C  44 
 TRP   0.006   0.001   TRP A 346 
 HIS   0.005   0.001   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 9268)
  covalent geometry    : angle       0.47010 (12660)
  hydrogen bonds       : bond        0.05771 (  407)
  hydrogen bonds       : angle       4.54609 ( 1114)
  metal coordination   : bond        0.00905 (    4)
  metal coordination   : angle       2.10680 (    2)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 0.475 
Fit side-chains
   revert: symmetry clash
REVERT: A  255 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.7729 (mtt)
REVERT: B  151 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8714 (mttp)
REVERT: C   54 LYS cc_start: 0.8511 (tppt) cc_final: 0.8208 (mmmt)
REVERT: C   59 LEU cc_start: 0.9559 (OUTLIER) cc_final: 0.9325 (mt)
REVERT: C   66 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7640 (mp0)
  outliers start: 17
  outliers final: 5
  residues processed: 100
  average time/residue: 1.4192
  time to fit residues: 150.9193
Evaluate side-chains
  94 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 85
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 GLU
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  255 MET
Chi-restraints excluded: chain B residue  151 LYS
Chi-restraints excluded: chain B residue  444 ASP
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain C residue   59 LEU
Chi-restraints excluded: chain C residue   66 GLU
Chi-restraints excluded: chain C residue   75 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 36 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0570
   chunk 82 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 58 optimal weight:    1.9990
   chunk 95 optimal weight:    1.9990
   chunk 91 optimal weight:    3.9990
   chunk 88 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.7902

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

Flipped N/Q/H residues before XYZ refinement:
A 195 ASN
B 491 GLN
C  96 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.112736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.077368 restraints weight = 34716.712|
|-----------------------------------------------------------------------------|
r_work (start): 0.2839 rms_B_bonded: 1.95
r_work: 0.2713 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2587 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.2587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8927
moved from start:          0.0827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9272  Z= 0.116
  Angle     :  0.445   4.064  12662  Z= 0.232
  Chirality :  0.036   0.166   1445
  Planarity :  0.003   0.048   1525
  Dihedral  : 11.227  73.535   1604
  Min Nonbonded Distance : 1.853

Molprobity Statistics.
  All-atom Clashscore : 1.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 21.51 %
    Favored  : 76.34 %
  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 aren not related in a simple way.
  whole:  1.49 (0.26), residues: 1065
  helix:  2.02 (0.25), residues: 459
  sheet:  0.85 (0.55), residues: 85
  loop :  0.14 (0.27), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 133 
 TYR   0.012   0.001   TYR A 403 
 PHE   0.010   0.001   PHE C  44 
 TRP   0.006   0.001   TRP A 346 
 HIS   0.004   0.001   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 9268)
  covalent geometry    : angle       0.44442 (12660)
  hydrogen bonds       : bond        0.05392 (  407)
  hydrogen bonds       : angle       4.27231 ( 1114)
  metal coordination   : bond        0.00468 (    4)
  metal coordination   : angle       2.05682 (    2)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 91
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
REVERT: A  255 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.7833 (mtt)
REVERT: B   38 MET cc_start: 0.9186 (tpt) cc_final: 0.8721 (tpt)
REVERT: B  151 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8696 (mttp)
REVERT: C   54 LYS cc_start: 0.8524 (tppt) cc_final: 0.8237 (mmmt)
REVERT: C   66 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7654 (mp0)
  outliers start: 20
  outliers final: 6
  residues processed: 104
  average time/residue: 1.4683
  time to fit residues: 161.9630
Evaluate side-chains
  97 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 88
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 GLU
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  255 MET
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue  151 LYS
Chi-restraints excluded: chain B residue  444 ASP
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain C residue   66 GLU
Chi-restraints excluded: chain C residue   75 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 103 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 1 optimal weight:    4.9990
   chunk 66 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9980
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 195 ASN
B 491 GLN
C   3 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.111103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.075514 restraints weight = 34698.700|
|-----------------------------------------------------------------------------|
r_work (start): 0.2806 rms_B_bonded: 1.95
r_work: 0.2681 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2555 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.2555
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8951
moved from start:          0.1044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   9272  Z= 0.175
  Angle     :  0.469   4.256  12662  Z= 0.247
  Chirality :  0.037   0.163   1445
  Planarity :  0.004   0.050   1525
  Dihedral  : 11.278  73.587   1604
  Min Nonbonded Distance : 1.824

Molprobity Statistics.
  All-atom Clashscore : 1.74
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.63 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 22.15 %
    Favored  : 75.81 %
  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 aren not related in a simple way.
  whole:  1.37 (0.25), residues: 1065
  helix:  1.88 (0.24), residues: 459
  sheet:  0.76 (0.55), residues: 85
  loop :  0.13 (0.27), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 133 
 TYR   0.014   0.001   TYR A 403 
 PHE   0.015   0.001   PHE C  44 
 TRP   0.006   0.001   TRP A 346 
 HIS   0.004   0.001   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 9268)
  covalent geometry    : angle       0.46831 (12660)
  hydrogen bonds       : bond        0.05752 (  407)
  hydrogen bonds       : angle       4.26703 ( 1114)
  metal coordination   : bond        0.00972 (    4)
  metal coordination   : angle       1.72337 (    2)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 87
  time to evaluate  : 0.407 
Fit side-chains
REVERT: A  409 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.8518 (ttm110)
REVERT: B   38 MET cc_start: 0.9239 (tpt) cc_final: 0.8755 (tpt)
REVERT: B  151 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8665 (mttp)
REVERT: C   54 LYS cc_start: 0.8550 (tppt) cc_final: 0.8254 (mmmt)
REVERT: C   66 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7690 (mp0)
  outliers start: 19
  outliers final: 9
  residues processed: 100
  average time/residue: 1.4023
  time to fit residues: 148.9691
Evaluate side-chains
  98 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 GLU
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  255 MET
Chi-restraints excluded: chain A residue  409 ARG
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   59 GLU
Chi-restraints excluded: chain B residue  151 LYS
Chi-restraints excluded: chain B residue  444 ASP
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain C residue   66 GLU
Chi-restraints excluded: chain C residue   75 LYS
Chi-restraints excluded: chain C residue  125 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 90 optimal weight:    4.9990
   chunk 54 optimal weight:    0.9980
   chunk 105 optimal weight:    3.9990
   chunk 2 optimal weight:   10.0000
   chunk 9 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 28 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   chunk 7 optimal weight:    4.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 195 ASN
B 211 ASN
B 491 GLN
C   3 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.110794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2819 r_free = 0.2819 target = 0.075377 restraints weight = 34608.242|
|-----------------------------------------------------------------------------|
r_work (start): 0.2803 rms_B_bonded: 1.94
r_work: 0.2677 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2552 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.2552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8953
moved from start:          0.1127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9272  Z= 0.170
  Angle     :  0.463   4.234  12662  Z= 0.244
  Chirality :  0.037   0.158   1445
  Planarity :  0.004   0.049   1525
  Dihedral  : 11.293  73.571   1604
  Min Nonbonded Distance : 1.827

Molprobity Statistics.
  All-atom Clashscore : 1.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 21.29 %
    Favored  : 76.34 %
  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 aren not related in a simple way.
  whole:  1.29 (0.25), residues: 1065
  helix:  1.83 (0.24), residues: 459
  sheet:  0.72 (0.55), residues: 85
  loop :  0.07 (0.26), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 133 
 TYR   0.014   0.001   TYR A 403 
 PHE   0.015   0.001   PHE C  44 
 TRP   0.005   0.001   TRP A 346 
 HIS   0.004   0.001   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 9268)
  covalent geometry    : angle       0.46229 (12660)
  hydrogen bonds       : bond        0.05697 (  407)
  hydrogen bonds       : angle       4.24322 ( 1114)
  metal coordination   : bond        0.00901 (    4)
  metal coordination   : angle       1.88544 (    2)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 89
  time to evaluate  : 0.530 
Fit side-chains
REVERT: A  119 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.8894 (mtp180)
REVERT: A  409 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8515 (ttm110)
REVERT: B   38 MET cc_start: 0.9234 (tpt) cc_final: 0.8744 (tpt)
REVERT: B  151 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8669 (mttp)
REVERT: C   54 LYS cc_start: 0.8549 (tppt) cc_final: 0.8245 (mmmt)
REVERT: C   66 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7718 (mp0)
  outliers start: 22
  outliers final: 11
  residues processed: 104
  average time/residue: 1.5055
  time to fit residues: 165.9600
Evaluate side-chains
  102 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 87
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 ARG
Chi-restraints excluded: chain A residue  135 GLU
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  255 MET
Chi-restraints excluded: chain A residue  409 ARG
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   59 GLU
Chi-restraints excluded: chain B residue   75 CYS
Chi-restraints excluded: chain B residue  151 LYS
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  444 ASP
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain C residue   66 GLU
Chi-restraints excluded: chain C residue   75 LYS
Chi-restraints excluded: chain C residue  123 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 89 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 95 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 72 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 71 optimal weight:    0.9980
   chunk 80 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
A 195 ASN
B 491 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.110989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2823 r_free = 0.2823 target = 0.075642 restraints weight = 34507.663|
|-----------------------------------------------------------------------------|
r_work (start): 0.2809 rms_B_bonded: 1.94
r_work: 0.2685 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2560 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.2560
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8949
moved from start:          0.1237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9272  Z= 0.150
  Angle     :  0.454   4.179  12662  Z= 0.239
  Chirality :  0.036   0.156   1445
  Planarity :  0.004   0.050   1525
  Dihedral  : 11.277  73.535   1604
  Min Nonbonded Distance : 1.836

Molprobity Statistics.
  All-atom Clashscore : 1.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 21.51 %
    Favored  : 76.45 %
  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 aren not related in a simple way.
  whole:  1.42 (0.25), residues: 1065
  helix:  1.99 (0.24), residues: 452
  sheet:  0.68 (0.54), residues: 87
  loop :  0.13 (0.27), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 133 
 TYR   0.013   0.001   TYR A 403 
 PHE   0.014   0.001   PHE C  44 
 TRP   0.005   0.001   TRP A 346 
 HIS   0.004   0.001   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 9268)
  covalent geometry    : angle       0.45306 (12660)
  hydrogen bonds       : bond        0.05566 (  407)
  hydrogen bonds       : angle       4.19677 ( 1114)
  metal coordination   : bond        0.00777 (    4)
  metal coordination   : angle       1.82945 (    2)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 86
  time to evaluate  : 0.492 
Fit side-chains
REVERT: A  119 ARG cc_start: 0.9155 (OUTLIER) cc_final: 0.8891 (mtp180)
REVERT: A  409 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8537 (ttm110)
REVERT: B   38 MET cc_start: 0.9195 (tpt) cc_final: 0.8716 (tpt)
REVERT: B  151 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8670 (mttp)
REVERT: C   54 LYS cc_start: 0.8551 (tppt) cc_final: 0.8249 (mmmt)
REVERT: C   66 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7734 (mp0)
  outliers start: 19
  outliers final: 9
  residues processed: 99
  average time/residue: 1.5174
  time to fit residues: 159.1341
Evaluate side-chains
  99 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 ARG
Chi-restraints excluded: chain A residue  135 GLU
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  409 ARG
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   59 GLU
Chi-restraints excluded: chain B residue   75 CYS
Chi-restraints excluded: chain B residue  151 LYS
Chi-restraints excluded: chain B residue  444 ASP
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain C residue   66 GLU
Chi-restraints excluded: chain C residue   75 LYS
Chi-restraints excluded: chain C residue  123 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 83 optimal weight:    1.9990
   chunk 102 optimal weight:    2.9990
   chunk 2 optimal weight:    9.9990
   chunk 6 optimal weight:    7.9990
   chunk 75 optimal weight:    2.9990
   chunk 105 optimal weight:    3.9990
   chunk 85 optimal weight:    0.9990
   chunk 88 optimal weight:    0.0570
   chunk 24 optimal weight:    0.9990
   chunk 81 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9980
   overall best weight:    1.0104

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

Flipped N/Q/H residues before XYZ refinement:
A 195 ASN
B 211 ASN
B 491 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.111159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2818 r_free = 0.2818 target = 0.075509 restraints weight = 34836.555|
|-----------------------------------------------------------------------------|
r_work (start): 0.2801 rms_B_bonded: 1.94
r_work: 0.2678 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2553 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.2553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8941
moved from start:          0.1301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9272  Z= 0.136
  Angle     :  0.447   4.128  12662  Z= 0.235
  Chirality :  0.036   0.155   1445
  Planarity :  0.004   0.049   1525
  Dihedral  : 11.250  73.522   1604
  Min Nonbonded Distance : 1.843

Molprobity Statistics.
  All-atom Clashscore : 1.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 21.08 %
    Favored  : 76.56 %
  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 aren not related in a simple way.
  whole:  1.46 (0.26), residues: 1065
  helix:  2.03 (0.24), residues: 452
  sheet:  0.75 (0.54), residues: 87
  loop :  0.14 (0.27), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 133 
 TYR   0.013   0.001   TYR A 403 
 PHE   0.013   0.001   PHE C  44 
 TRP   0.005   0.001   TRP A 346 
 HIS   0.004   0.001   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 9268)
  covalent geometry    : angle       0.44645 (12660)
  hydrogen bonds       : bond        0.05457 (  407)
  hydrogen bonds       : angle       4.14723 ( 1114)
  metal coordination   : bond        0.00669 (    4)
  metal coordination   : angle       1.88756 (    2)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 88
  time to evaluate  : 0.523 
Fit side-chains
REVERT: A  409 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8509 (ttm110)
REVERT: B  127 ASP cc_start: 0.8790 (m-30) cc_final: 0.8511 (m-30)
REVERT: B  151 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8638 (mttp)
REVERT: C   54 LYS cc_start: 0.8544 (tppt) cc_final: 0.8233 (mmmt)
REVERT: C   66 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7758 (mp0)
  outliers start: 22
  outliers final: 9
  residues processed: 103
  average time/residue: 1.3608
  time to fit residues: 149.0892
Evaluate side-chains
  101 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 GLU
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  409 ARG
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   59 GLU
Chi-restraints excluded: chain B residue   75 CYS
Chi-restraints excluded: chain B residue  151 LYS
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  444 ASP
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain C residue   66 GLU
Chi-restraints excluded: chain C residue   75 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 17 optimal weight:    0.2980
   chunk 57 optimal weight:    0.5980
   chunk 37 optimal weight:    1.9990
   chunk 9 optimal weight:    0.0060
   chunk 55 optimal weight:    2.9990
   chunk 21 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9990
   chunk 7 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9990
   chunk 58 optimal weight:    0.7980
   chunk 32 optimal weight:    0.7980
   overall best weight:    0.4596

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

Flipped N/Q/H residues before XYZ refinement:
A 195 ASN
B 491 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.113013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.077754 restraints weight = 34564.070|
|-----------------------------------------------------------------------------|
r_work (start): 0.2839 rms_B_bonded: 1.94
r_work: 0.2716 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2591 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.2591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8914
moved from start:          0.1342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   9272  Z= 0.090
  Angle     :  0.427   4.035  12662  Z= 0.223
  Chirality :  0.035   0.150   1445
  Planarity :  0.003   0.051   1525
  Dihedral  : 11.134  73.422   1604
  Min Nonbonded Distance : 1.885

Molprobity Statistics.
  All-atom Clashscore : 1.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 21.72 %
    Favored  : 76.56 %
  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 aren not related in a simple way.
  whole:  1.68 (0.26), residues: 1065
  helix:  2.25 (0.25), residues: 452
  sheet:  0.88 (0.55), residues: 87
  loop :  0.22 (0.27), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 133 
 TYR   0.010   0.001   TYR A 403 
 PHE   0.007   0.001   PHE C  44 
 TRP   0.005   0.001   TRP A 346 
 HIS   0.004   0.001   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00206 ( 9268)
  covalent geometry    : angle       0.42604 (12660)
  hydrogen bonds       : bond        0.05035 (  407)
  hydrogen bonds       : angle       3.99807 ( 1114)
  metal coordination   : bond        0.00274 (    4)
  metal coordination   : angle       2.11697 (    2)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.490 
Fit side-chains
REVERT: A  409 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8474 (ttm110)
REVERT: B  127 ASP cc_start: 0.8712 (m-30) cc_final: 0.8470 (m-30)
REVERT: B  151 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8665 (mttp)
REVERT: B  235 MET cc_start: 0.9247 (mmp) cc_final: 0.8866 (mmp)
REVERT: B  302 ARG cc_start: 0.8494 (mmm-85) cc_final: 0.8232 (mmm160)
REVERT: B  487 ARG cc_start: 0.7873 (tpm-80) cc_final: 0.7552 (tpm170)
REVERT: C   54 LYS cc_start: 0.8539 (tppt) cc_final: 0.8271 (mmtp)
REVERT: C   66 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7724 (mp0)
REVERT: C  100 ASP cc_start: 0.8753 (t0) cc_final: 0.8409 (t0)
  outliers start: 16
  outliers final: 9
  residues processed: 102
  average time/residue: 1.3831
  time to fit residues: 149.9100
Evaluate side-chains
  99 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  409 ARG
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   59 GLU
Chi-restraints excluded: chain B residue   75 CYS
Chi-restraints excluded: chain B residue  151 LYS
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  444 ASP
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain C residue   66 GLU
Chi-restraints excluded: chain C residue   75 LYS
Chi-restraints excluded: chain C residue  123 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9980
   chunk 17 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9990
   chunk 102 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 106 optimal weight:    7.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 195 ASN
B 211 ASN
B 491 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.111821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.076202 restraints weight = 34494.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.2814 rms_B_bonded: 1.96
r_work: 0.2689 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2566 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.2566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8931
moved from start:          0.1411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9272  Z= 0.127
  Angle     :  0.438   4.638  12662  Z= 0.230
  Chirality :  0.036   0.151   1445
  Planarity :  0.004   0.051   1525
  Dihedral  : 11.162  73.509   1604
  Min Nonbonded Distance : 1.838

Molprobity Statistics.
  All-atom Clashscore : 1.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 21.83 %
    Favored  : 76.56 %
  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 aren not related in a simple way.
  whole:  1.59 (0.26), residues: 1065
  helix:  2.19 (0.25), residues: 452
  sheet:  0.50 (0.53), residues: 93
  loop :  0.22 (0.27), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 133 
 TYR   0.012   0.001   TYR A 403 
 PHE   0.012   0.001   PHE C  44 
 TRP   0.005   0.001   TRP A 346 
 HIS   0.004   0.001   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 9268)
  covalent geometry    : angle       0.43791 (12660)
  hydrogen bonds       : bond        0.05301 (  407)
  hydrogen bonds       : angle       4.04369 ( 1114)
  metal coordination   : bond        0.00644 (    4)
  metal coordination   : angle       1.72999 (    2)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 88
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
REVERT: A  409 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8480 (ttm110)
REVERT: B  151 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8660 (mttp)
REVERT: B  235 MET cc_start: 0.9238 (mmp) cc_final: 0.8885 (mmp)
REVERT: B  487 ARG cc_start: 0.7859 (tpm-80) cc_final: 0.7641 (tpm170)
REVERT: C   54 LYS cc_start: 0.8551 (tppt) cc_final: 0.8263 (mmmt)
REVERT: C   66 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7726 (mp0)
REVERT: C  100 ASP cc_start: 0.8815 (t0) cc_final: 0.8459 (t0)
  outliers start: 15
  outliers final: 10
  residues processed: 98
  average time/residue: 1.3569
  time to fit residues: 141.4330
Evaluate side-chains
  101 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  409 ARG
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   59 GLU
Chi-restraints excluded: chain B residue   75 CYS
Chi-restraints excluded: chain B residue  151 LYS
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  444 ASP
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain C residue   66 GLU
Chi-restraints excluded: chain C residue   75 LYS
Chi-restraints excluded: chain C residue  123 ASP
Chi-restraints excluded: chain C residue  125 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 65 optimal weight:    1.9990
   chunk 87 optimal weight:    2.9990
   chunk 6 optimal weight:    0.1980
   chunk 14 optimal weight:    0.5980
   chunk 45 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 57 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 195 ASN
B 211 ASN
B 491 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.112346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.076879 restraints weight = 34371.836|
|-----------------------------------------------------------------------------|
r_work (start): 0.2826 rms_B_bonded: 1.95
r_work: 0.2704 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2578 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.2578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8924
moved from start:          0.1435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9272  Z= 0.107
  Angle     :  0.434   4.676  12662  Z= 0.227
  Chirality :  0.035   0.153   1445
  Planarity :  0.004   0.053   1525
  Dihedral  : 11.146  73.483   1604
  Min Nonbonded Distance : 1.858

Molprobity Statistics.
  All-atom Clashscore : 1.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 22.04 %
    Favored  : 76.34 %
  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 aren not related in a simple way.
  whole:  1.66 (0.26), residues: 1065
  helix:  2.24 (0.25), residues: 452
  sheet:  0.63 (0.54), residues: 91
  loop :  0.24 (0.27), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 133 
 TYR   0.011   0.001   TYR A 403 
 PHE   0.010   0.001   PHE C  44 
 TRP   0.005   0.001   TRP A 346 
 HIS   0.004   0.001   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 9268)
  covalent geometry    : angle       0.43381 (12660)
  hydrogen bonds       : bond        0.05174 (  407)
  hydrogen bonds       : angle       4.00579 ( 1114)
  metal coordination   : bond        0.00499 (    4)
  metal coordination   : angle       1.83084 (    2)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 88
  time to evaluate  : 0.480 
Fit side-chains
REVERT: A  409 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8497 (ttm110)
REVERT: B  235 MET cc_start: 0.9240 (mmp) cc_final: 0.8901 (mmp)
REVERT: B  487 ARG cc_start: 0.7849 (tpm-80) cc_final: 0.7633 (tpm170)
REVERT: C   54 LYS cc_start: 0.8546 (tppt) cc_final: 0.8259 (mmmt)
REVERT: C   66 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7733 (mp0)
REVERT: C  100 ASP cc_start: 0.8803 (t0) cc_final: 0.8439 (t0)
  outliers start: 15
  outliers final: 9
  residues processed: 99
  average time/residue: 1.3887
  time to fit residues: 146.4167
Evaluate side-chains
  97 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  409 ARG
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   59 GLU
Chi-restraints excluded: chain B residue   75 CYS
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  444 ASP
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain C residue   66 GLU
Chi-restraints excluded: chain C residue   75 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 100 optimal weight:    0.0040
   chunk 92 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 82 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 101 optimal weight:    0.6980
   chunk 77 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9990
   overall best weight:    0.6794

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

Flipped N/Q/H residues before XYZ refinement:
A 195 ASN
B 491 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.112468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.076874 restraints weight = 34686.667|
|-----------------------------------------------------------------------------|
r_work (start): 0.2829 rms_B_bonded: 1.97
r_work: 0.2706 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2580 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8923
moved from start:          0.1473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9272  Z= 0.106
  Angle     :  0.433   5.040  12662  Z= 0.227
  Chirality :  0.035   0.152   1445
  Planarity :  0.004   0.053   1525
  Dihedral  : 11.124  73.485   1604
  Min Nonbonded Distance : 1.860

Molprobity Statistics.
  All-atom Clashscore : 1.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 22.26 %
    Favored  : 76.24 %
  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 aren not related in a simple way.
  whole:  1.69 (0.26), residues: 1065
  helix:  2.28 (0.25), residues: 452
  sheet:  0.62 (0.54), residues: 91
  loop :  0.24 (0.27), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 133 
 TYR   0.011   0.001   TYR A 403 
 PHE   0.010   0.001   PHE C  44 
 TRP   0.005   0.001   TRP A 346 
 HIS   0.004   0.001   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 9268)
  covalent geometry    : angle       0.43242 (12660)
  hydrogen bonds       : bond        0.05137 (  407)
  hydrogen bonds       : angle       3.97885 ( 1114)
  metal coordination   : bond        0.00464 (    4)
  metal coordination   : angle       1.75241 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6203.22 seconds
wall clock time: 105 minutes 40.67 seconds (6340.67 seconds total)