Starting phenix.real_space_refine
on Thu Jun 19 06:49:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pt2_17866/06_2025/8pt2_17866.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pt2_17866/06_2025/8pt2_17866.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.59
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pt2_17866/06_2025/8pt2_17866.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pt2_17866/06_2025/8pt2_17866.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pt2_17866/06_2025/8pt2_17866.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pt2_17866/06_2025/8pt2_17866.cif"
  }
  resolution = 2.59
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     Zn      3      6.06       5
     P      27      5.49       5
     S      63      5.16       5
     C    6950      2.51       5
     N    1972      2.21       5
     O    2175      1.98       5
     H   10901      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 22091
  Number of models: 1
  Model: ""
    Number of chains: 8
    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: 7900
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 512, 7900
          Classifications: {'peptide': 512}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 490}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 6676
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 426, 6676
          Classifications: {'peptide': 426}
          Link IDs: {'PTRANS': 22, 'TRANS': 403}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "V"
      Number of atoms: 406
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 406
          Classifications: {'RNA': 13}
          Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 2, 'rna3p_pyr': 6}
          Link IDs: {'rna2p': 5, 'rna3p': 7}
    Chain: "D"
      Number of atoms: 453
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 453
          Classifications: {'RNA': 14}
          Modifications used: {'3*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 6, 'rna3p_pyr': 3}
          Link IDs: {'rna2p': 4, 'rna3p': 9}
          Chain breaks: 1
    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: "C"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2585  SG  CYS A 161      46.153  53.513  18.541  1.00 47.15           S
  ATOM   4473  SG  CYS A 282      43.740  52.013  15.789  1.00 59.75           S
  ATOM  18156  SG  CYS C 233      22.092  62.596 107.997  1.00 74.16           S
  ATOM  18180  SG  CYS C 235      22.631  64.040 104.434  1.00 71.02           S
  ATOM  16822  SG  CYS C 146      10.935  72.545  88.479  1.00 81.71           S
  ATOM  17010  SG  CYS C 159      11.925  75.602  90.433  1.00 89.66           S
  ATOM  17066  SG  CYS C 163      14.226  72.636  90.449  1.00 72.58           S
  ATOM  17076  SG  CYS C 164      13.852  74.746  87.284  1.00 73.55           S

  Time building chain proxies: 10.33, per 1000 atoms: 0.47
  Number of scatterers: 22091
  At special positions: 0
  Unit cell: (92.4, 110.88, 125.16, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      3     29.99
     S      63     16.00
     P      27     15.00
     O    2175      8.00
     N    1972      7.00
     C    6950      6.00
     H   10901      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: 5.27
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  
  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 161 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 282 "
      pdb="  ZN C 501 "
        pdb="ZN    ZN C 501 " - pdb=" NE2 HIS C 191 "
        pdb="ZN    ZN C 501 " - pdb=" ND1 HIS C 184 "
        pdb="ZN    ZN C 501 " - pdb=" SG  CYS C 233 "
        pdb="ZN    ZN C 501 " - pdb=" SG  CYS C 235 "
      pdb="  ZN C 502 "
        pdb="ZN    ZN C 502 " - pdb=" SG  CYS C 159 "
        pdb="ZN    ZN C 502 " - pdb=" SG  CYS C 163 "
        pdb="ZN    ZN C 502 " - pdb=" SG  CYS C 146 "
        pdb="ZN    ZN C 502 " - pdb=" SG  CYS C 164 "
      Number of angles added : 9


  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2544

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 15 sheets defined
      42.1% alpha, 14.2% beta
      6 base pairs and 11 stacking pairs defined.
    Time for finding SS restraints: 11.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 4
      No H-bonds generated for 'chain 'A' and resid 2 through 4'
    Processing helix  chain 'A' and resid 5 through 13
    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: 3.515A  pdb=" N   ILE A 145 " --> pdb=" O   ARG A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 169
    Processing helix  chain 'A' and resid 174 through 189
    Processing helix  chain 'A' and resid 223 through 234
    Processing helix  chain 'A' and resid 301 through 310
    Processing helix  chain 'A' and resid 312 through 323
      removed outlier: 4.431A  pdb=" N   ASP A 323 " --> pdb=" O   ILE A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 344 through 356
    Processing helix  chain 'A' and resid 359 through 374
      removed outlier: 3.893A  pdb=" N   ALA A 363 " --> pdb=" O   ARG A 359 " (cutoff:3.500A)
    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: 3.565A  pdb=" N   GLN B   5 " --> pdb=" O   TRP B   2 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 23 through 39
    Processing helix  chain 'B' and resid 66 through 70
    Processing helix  chain 'B' and resid 92 through 103
    Processing helix  chain 'B' and resid 107 through 118
    Processing helix  chain 'B' and resid 129 through 138
      removed outlier: 3.654A  pdb=" N   ARG B 138 " --> pdb=" O   LEU B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 161 through 183
      removed outlier: 3.590A  pdb=" N   VAL B 170 " --> pdb=" O   LEU B 166 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 191 through 203
    Processing helix  chain 'B' and resid 204 through 206
      No H-bonds generated for 'chain 'B' and resid 204 through 206'
    Processing helix  chain 'B' and resid 216 through 221
      removed outlier: 3.552A  pdb=" N   ILE B 221 " --> pdb=" O   TYR B 217 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 234
    Processing helix  chain 'B' and resid 235 through 248
      removed outlier: 3.612A  pdb=" N   GLY B 239 " --> pdb=" O   MET B 235 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 279
      removed outlier: 3.733A  pdb=" N   LEU B 277 " --> pdb=" O   ALA B 273 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 297 through 311
    Processing helix  chain 'B' and resid 356 through 372
    Processing helix  chain 'B' and resid 376 through 396
    Processing helix  chain 'B' and resid 409 through 413
      removed outlier: 3.563A  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: 4.069A  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 497
    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 33 through 40
    Processing helix  chain 'C' and resid 42 through 54
    Processing helix  chain 'C' and resid 55 through 59
    Processing helix  chain 'C' and resid 87 through 97
    Processing helix  chain 'C' and resid 100 through 107
    Processing helix  chain 'C' and resid 145 through 151
      removed outlier: 3.773A  pdb=" N   VAL C 151 " --> pdb=" O   GLU C 147 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 208 through 219
    Processing helix  chain 'C' and resid 234 through 241
    Processing helix  chain 'C' and resid 281 through 289
    Processing helix  chain 'C' and resid 303 through 317
      removed outlier: 4.168A  pdb=" N   ARG C 317 " --> pdb=" O   ALA C 313 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 319 through 334
    Processing helix  chain 'C' and resid 350 through 356
      removed outlier: 3.762A  pdb=" N   LEU C 354 " --> pdb=" O   ASN C 350 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   SER C 356 " --> pdb=" O   LYS C 352 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 370 through 376
    Processing helix  chain 'C' and resid 421 through 426
    Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 18
    Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 27
      removed outlier: 6.726A  pdb=" N   TRP A  52 " --> pdb=" O   VAL A  69 " (cutoff:3.500A)
      removed outlier: 7.726A  pdb=" N   CYS A  71 " --> pdb=" O   TRP A  52 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   ALA A  54 " --> pdb=" O   CYS A  71 " (cutoff:3.500A)
      removed outlier: 7.517A  pdb=" N   LEU A  73 " --> pdb=" O   ALA A  54 " (cutoff:3.500A)
      removed outlier: 6.960A  pdb=" N   GLU A  56 " --> pdb=" O   LEU A  73 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   THR A  78 " --> pdb=" O   ASN A  74 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 137
    Processing sheet with id=AA4, first strand: chain 'A' and resid 136 through 137
    Processing sheet with id=AA5, first strand: chain 'A' and resid 192 through 194
      removed outlier: 6.314A  pdb=" N   TRP A 198 " --> pdb=" O   ALA A 251 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 192 through 194
      removed outlier: 6.314A  pdb=" N   TRP A 198 " --> pdb=" O   ALA A 251 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   SER A 248 " --> pdb=" O   LEU A 277 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   LEU A 277 " --> pdb=" O   SER A 248 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   HIS A 271 " --> pdb=" O   VAL A 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 74 through 80
    Processing sheet with id=AA8, first strand: chain 'B' and resid 155 through 159
      removed outlier: 7.100A  pdb=" N   PHE B 140 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 326 through 329
    Processing sheet with id=AB1, first strand: chain 'B' and resid 477 through 478
    Processing sheet with id=AB2, first strand: chain 'C' and resid 71 through 72
    Processing sheet with id=AB3, first strand: chain 'C' and resid 77 through 83
    Processing sheet with id=AB4, first strand: chain 'C' and resid 221 through 224
      removed outlier: 6.848A  pdb=" N   GLY C 262 " --> pdb=" O   PHE C 258 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 360 through 363
    Processing sheet with id=AB6, first strand: chain 'C' and resid 383 through 388
      removed outlier: 6.669A  pdb=" N   MET C 415 " --> pdb=" O   LEU C 387 " (cutoff:3.500A)

    490 hydrogen bonds defined for protein.
    1344 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      15 hydrogen bonds
      30 hydrogen bond angles
      0 basepair planarities
      6 basepair parallelities
      11 stacking parallelities
  Total time for adding SS restraints: 8.60

  Time building geometry restraints manager: 6.52 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: 10869
        1.03 -     1.23: 43
        1.23 -     1.42: 4830
        1.42 -     1.62: 6544
        1.62 -     1.81: 86
  Bond restraints: 22372
  Sorted by residual:
  bond pdb=" C   LEU B 167 "
       pdb=" O   LEU B 167 "
    ideal  model  delta    sigma   weight residual
    1.237  1.245 -0.008 1.19e-02 7.06e+03 4.71e-01
  bond pdb=" CB  LYS C 352 "
       pdb=" CG  LYS C 352 "
    ideal  model  delta    sigma   weight residual
    1.520  1.540 -0.020 3.00e-02 1.11e+03 4.34e-01
  bond pdb=" CB  GLU C 181 "
       pdb=" CG  GLU C 181 "
    ideal  model  delta    sigma   weight residual
    1.520  1.539 -0.019 3.00e-02 1.11e+03 4.19e-01
  bond pdb=" CG  PRO C 252 "
       pdb=" CD  PRO C 252 "
    ideal  model  delta    sigma   weight residual
    1.503  1.482  0.021 3.40e-02 8.65e+02 3.96e-01
  bond pdb=" CG  PRO B 502 "
       pdb=" CD  PRO B 502 "
    ideal  model  delta    sigma   weight residual
    1.503  1.482  0.021 3.40e-02 8.65e+02 3.68e-01
  ... (remaining 22367 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.83: 36391
        0.83 -     1.65: 3643
        1.65 -     2.48: 245
        2.48 -     3.31: 99
        3.31 -     4.13: 30
  Bond angle restraints: 40408
  Sorted by residual:
  angle pdb=" N   LYS C 199 "
        pdb=" CA  LYS C 199 "
        pdb=" C   LYS C 199 "
      ideal   model   delta    sigma   weight residual
     114.09  111.09    3.00 1.55e+00 4.16e-01 3.75e+00
  angle pdb=" CG  ARG B 487 "
        pdb=" CD  ARG B 487 "
        pdb=" NE  ARG B 487 "
      ideal   model   delta    sigma   weight residual
     112.00  116.13   -4.13 2.20e+00 2.07e-01 3.53e+00
  angle pdb=" CG  ARG A 154 "
        pdb=" CD  ARG A 154 "
        pdb=" NE  ARG A 154 "
      ideal   model   delta    sigma   weight residual
     112.00  115.79   -3.79 2.20e+00 2.07e-01 2.96e+00
  angle pdb=" CD  ARG B 487 "
        pdb=" NE  ARG B 487 "
        pdb=" CZ  ARG B 487 "
      ideal   model   delta    sigma   weight residual
     124.40  126.76   -2.36 1.40e+00 5.10e-01 2.84e+00
  angle pdb=" CG  LYS A 147 "
        pdb=" CD  LYS A 147 "
        pdb=" CE  LYS A 147 "
      ideal   model   delta    sigma   weight residual
     111.30  115.17   -3.87 2.30e+00 1.89e-01 2.83e+00
  ... (remaining 40403 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 9343
       17.98 -    35.95: 788
       35.95 -    53.93: 308
       53.93 -    71.90: 91
       71.90 -    89.88: 31
  Dihedral angle restraints: 10561
    sinusoidal: 5981
      harmonic: 4580
  Sorted by residual:
  dihedral pdb=" CG  ARG B 487 "
           pdb=" CD  ARG B 487 "
           pdb=" NE  ARG B 487 "
           pdb=" CZ  ARG B 487 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00  -39.92  -50.08     2      1.50e+01 4.44e-03 1.25e+01
  dihedral pdb=" CB  GLU C 115 "
           pdb=" CG  GLU C 115 "
           pdb=" CD  GLU C 115 "
           pdb=" OE1 GLU C 115 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.88   89.88     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CG  ARG B  63 "
           pdb=" CD  ARG B  63 "
           pdb=" NE  ARG B  63 "
           pdb=" CZ  ARG B  63 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  134.84  -44.84     2      1.50e+01 4.44e-03 1.06e+01
  ... (remaining 10558 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 1082
       0.025 -    0.051: 480
       0.051 -    0.076: 102
       0.076 -    0.102: 49
       0.102 -    0.127: 52
  Chirality restraints: 1765
  Sorted by residual:
  chirality pdb=" CA  ILE A 199 "
            pdb=" N   ILE A 199 "
            pdb=" C   ILE A 199 "
            pdb=" CB  ILE A 199 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.04e-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 3.97e-01
  chirality pdb=" CA  ILE A  53 "
            pdb=" N   ILE A  53 "
            pdb=" C   ILE A  53 "
            pdb=" CB  ILE A  53 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.95e-01
  ... (remaining 1762 not shown)

  Planarity restraints: 3219
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 487 "    0.150 9.50e-02 1.11e+02   5.03e-02 3.04e+00
        pdb=" NE  ARG B 487 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 487 "    0.008 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 487 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 487 "   -0.001 2.00e-02 2.50e+03
        pdb="HH11 ARG B 487 "   -0.006 2.00e-02 2.50e+03
        pdb="HH12 ARG B 487 "    0.001 2.00e-02 2.50e+03
        pdb="HH21 ARG B 487 "   -0.000 2.00e-02 2.50e+03
        pdb="HH22 ARG B 487 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B 501 "   -0.028 5.00e-02 4.00e+02   4.26e-02 2.91e+00
        pdb=" N   PRO B 502 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO B 502 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 502 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 217 "   -0.023 5.00e-02 4.00e+02   3.53e-02 2.00e+00
        pdb=" N   PRO A 218 "    0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO A 218 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 218 "   -0.020 5.00e-02 4.00e+02
  ... (remaining 3216 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.19: 1319
        2.19 -     2.80: 44023
        2.80 -     3.40: 60985
        3.40 -     4.00: 82553
        4.00 -     4.60: 125729
  Nonbonded interactions: 314609
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN B 397 "
            pdb=" HG1 THR B 399 "
     model   vdw
     1.593 2.450
  nonbonded pdb=" O   SER A 128 "
            pdb="HD22 ASN B  44 "
     model   vdw
     1.598 2.450
  nonbonded pdb=" H   GLY A 239 "
            pdb=" O   ALA A 251 "
     model   vdw
     1.628 2.450
  nonbonded pdb=" O   ALA C 330 "
            pdb=" HG1 THR C 334 "
     model   vdw
     1.662 2.450
  nonbonded pdb="HH21 ARG B 145 "
            pdb="HH11 ARG B 155 "
     model   vdw
     1.663 2.100
  ... (remaining 314604 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:             1.760
  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:             0.350
  Extract box with map and model:          0.790
  Check model and map are aligned:         0.160
  Set scattering table:                    0.220
  Process input model:                     64.700
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.080
  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:14.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   82.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8774
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   0.028  11483  Z= 0.096
  Angle     :  0.447   4.134  15638  Z= 0.232
  Chirality :  0.036   0.127   1765
  Planarity :  0.004   0.065   1918
  Dihedral  : 17.636  89.878   4454
  Min Nonbonded Distance : 1.885

Molprobity Statistics.
  All-atom Clashscore : 2.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 18.13 %
    Favored  : 80.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.23), residues: 1345
  helix:  2.08 (0.24), residues: 528
  sheet: -0.54 (0.42), residues: 130
  loop :  0.20 (0.24), residues: 687

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 263 
 HIS   0.004   0.001   HIS B 174 
 PHE   0.010   0.001   PHE C 175 
 TYR   0.010   0.001   TYR A 403 
 ARG   0.009   0.000   ARG B 487 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12071 (  490)
  hydrogen bonds       : angle       5.35624 ( 1374)
  metal coordination   : bond        0.00242 (   12)
  metal coordination   : angle       1.42684 (    9)
  covalent geometry    : bond        0.00216 (11471)
  covalent geometry    : angle       0.44567 (15629)

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

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

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 108
  time to evaluate  : 1.734 
Fit side-chains
   revert: symmetry clash
  outliers start: 16
  outliers final: 15
  residues processed: 124
  average time/residue: 3.4218
  time to fit residues: 452.2111
Evaluate side-chains
  124 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 109
  time to evaluate  : 1.556 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 SER
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain B residue   36 GLU
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  405 GLU
Chi-restraints excluded: chain B residue  444 ASP
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain C residue  151 VAL
Chi-restraints excluded: chain C residue  207 SER
Chi-restraints excluded: chain C residue  356 SER
Chi-restraints excluded: chain C residue  364 GLU
Chi-restraints excluded: chain C residue  388 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 114 optimal weight:    3.9990
   chunk 103 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 69 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9990
   chunk 106 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 79 optimal weight:    1.9990
   chunk 123 optimal weight:    4.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
A 195 ASN
B 330 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.108263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.083382 restraints weight = 39920.414|
|-----------------------------------------------------------------------------|
r_work (start): 0.2910 rms_B_bonded: 1.79
r_work: 0.2803 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.2687 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.2687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8815
moved from start:          0.0548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  11483  Z= 0.172
  Angle     :  0.502   4.103  15638  Z= 0.266
  Chirality :  0.038   0.133   1765
  Planarity :  0.004   0.041   1918
  Dihedral  : 11.538  80.085   1907
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 1.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 16.41 %
    Favored  : 81.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.23), residues: 1345
  helix:  1.99 (0.23), residues: 532
  sheet: -0.49 (0.41), residues: 128
  loop :  0.02 (0.23), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 346 
 HIS   0.006   0.001   HIS B 174 
 PHE   0.015   0.001   PHE C 175 
 TYR   0.015   0.001   TYR A 403 
 ARG   0.005   0.000   ARG B 487 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04711 (  490)
  hydrogen bonds       : angle       4.42894 ( 1374)
  metal coordination   : bond        0.00636 (   12)
  metal coordination   : angle       1.72265 (    9)
  covalent geometry    : bond        0.00395 (11471)
  covalent geometry    : angle       0.50085 (15629)

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

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

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 114
  time to evaluate  : 1.658 
Fit side-chains
   revert: symmetry clash
REVERT: C  356 SER cc_start: 0.8113 (OUTLIER) cc_final: 0.7733 (t)
  outliers start: 26
  outliers final: 18
  residues processed: 133
  average time/residue: 3.2504
  time to fit residues: 461.4274
Evaluate side-chains
  128 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 109
  time to evaluate  : 1.873 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 SER
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   78 THR
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  265 ARG
Chi-restraints excluded: chain A residue  317 ARG
Chi-restraints excluded: chain B residue   33 ARG
Chi-restraints excluded: chain B residue   36 GLU
Chi-restraints excluded: chain B residue   75 CYS
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  405 GLU
Chi-restraints excluded: chain B residue  444 ASP
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue  148 SER
Chi-restraints excluded: chain C residue  151 VAL
Chi-restraints excluded: chain C residue  156 THR
Chi-restraints excluded: chain C residue  207 SER
Chi-restraints excluded: chain C residue  301 SER
Chi-restraints excluded: chain C residue  356 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 127 optimal weight:    3.9990
   chunk 52 optimal weight:    0.3980
   chunk 31 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 113 optimal weight:    1.9990
   chunk 98 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 49 optimal weight:    4.9990
   chunk 17 optimal weight:    0.4980
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
A 195 ASN
B  44 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.108201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.083403 restraints weight = 39632.690|
|-----------------------------------------------------------------------------|
r_work (start): 0.2910 rms_B_bonded: 1.77
r_work: 0.2805 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.2693 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.2693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8813
moved from start:          0.0760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  11483  Z= 0.152
  Angle     :  0.489   4.101  15638  Z= 0.257
  Chirality :  0.038   0.133   1765
  Planarity :  0.004   0.044   1918
  Dihedral  : 11.341  83.500   1900
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 1.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 16.67 %
    Favored  : 81.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.23), residues: 1345
  helix:  1.92 (0.23), residues: 534
  sheet: -0.48 (0.41), residues: 128
  loop :  0.01 (0.23), residues: 683

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 263 
 HIS   0.005   0.001   HIS B 174 
 PHE   0.015   0.001   PHE C 175 
 TYR   0.014   0.001   TYR A 403 
 ARG   0.006   0.000   ARG A 265 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04470 (  490)
  hydrogen bonds       : angle       4.27901 ( 1374)
  metal coordination   : bond        0.00556 (   12)
  metal coordination   : angle       1.68008 (    9)
  covalent geometry    : bond        0.00350 (11471)
  covalent geometry    : angle       0.48766 (15629)

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

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

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 111
  time to evaluate  : 1.843 
Fit side-chains
   revert: symmetry clash
  outliers start: 24
  outliers final: 17
  residues processed: 130
  average time/residue: 3.2803
  time to fit residues: 456.2639
Evaluate side-chains
  125 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 108
  time to evaluate  : 1.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   78 THR
Chi-restraints excluded: chain A residue   83 GLU
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  265 ARG
Chi-restraints excluded: chain A residue  317 ARG
Chi-restraints excluded: chain B residue   33 ARG
Chi-restraints excluded: chain B residue   36 GLU
Chi-restraints excluded: chain B residue   75 CYS
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  405 GLU
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue  148 SER
Chi-restraints excluded: chain C residue  151 VAL
Chi-restraints excluded: chain C residue  156 THR
Chi-restraints excluded: chain C residue  301 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 62 optimal weight:    0.9990
   chunk 122 optimal weight:    2.9990
   chunk 107 optimal weight:    0.9990
   chunk 108 optimal weight:    0.6980
   chunk 27 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 123 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   overall best weight:    0.8786

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

Flipped N/Q/H residues before XYZ refinement:
A 195 ASN
B  44 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.109198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.084439 restraints weight = 39850.833|
|-----------------------------------------------------------------------------|
r_work (start): 0.2927 rms_B_bonded: 1.77
r_work: 0.2823 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.2711 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.2711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8799
moved from start:          0.0792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023  11483  Z= 0.112
  Angle     :  0.464   3.946  15638  Z= 0.242
  Chirality :  0.037   0.134   1765
  Planarity :  0.004   0.044   1918
  Dihedral  : 11.198  84.143   1895
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 1.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 16.58 %
    Favored  : 81.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.20 (0.23), residues: 1345
  helix:  2.09 (0.23), residues: 527
  sheet: -0.46 (0.42), residues: 128
  loop :  0.09 (0.23), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 209 
 HIS   0.004   0.001   HIS B 174 
 PHE   0.013   0.001   PHE C 175 
 TYR   0.013   0.001   TYR A 403 
 ARG   0.006   0.000   ARG B 487 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03916 (  490)
  hydrogen bonds       : angle       4.13878 ( 1374)
  metal coordination   : bond        0.00359 (   12)
  metal coordination   : angle       1.48689 (    9)
  covalent geometry    : bond        0.00254 (11471)
  covalent geometry    : angle       0.46283 (15629)

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

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

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 113
  time to evaluate  : 1.602 
Fit side-chains
   revert: symmetry clash
REVERT: B  148 GLU cc_start: 0.8078 (tt0) cc_final: 0.7507 (mt-10)
REVERT: C  108 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8705 (tt)
REVERT: C  352 LYS cc_start: 0.8038 (mmtm) cc_final: 0.7832 (mmtm)
  outliers start: 22
  outliers final: 12
  residues processed: 128
  average time/residue: 3.3639
  time to fit residues: 458.8333
Evaluate side-chains
  124 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 111
  time to evaluate  : 1.570 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 THR
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  265 ARG
Chi-restraints excluded: chain A residue  317 ARG
Chi-restraints excluded: chain B residue   33 ARG
Chi-restraints excluded: chain B residue   75 CYS
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  405 GLU
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  148 SER
Chi-restraints excluded: chain C residue  151 VAL
Chi-restraints excluded: chain C residue  301 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 91 optimal weight:    5.9990
   chunk 89 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 105 optimal weight:    2.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 195 ASN
B 330 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.106828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.082085 restraints weight = 39951.875|
|-----------------------------------------------------------------------------|
r_work (start): 0.2889 rms_B_bonded: 1.76
r_work: 0.2783 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.2671 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.2671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8833
moved from start:          0.1009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  11483  Z= 0.207
  Angle     :  0.527   4.243  15638  Z= 0.279
  Chirality :  0.039   0.138   1765
  Planarity :  0.004   0.047   1918
  Dihedral  : 11.241  87.400   1891
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 1.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 16.41 %
    Favored  : 81.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.22), residues: 1345
  helix:  1.69 (0.22), residues: 540
  sheet: -0.52 (0.41), residues: 128
  loop : -0.11 (0.23), residues: 677

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 263 
 HIS   0.007   0.001   HIS B 174 
 PHE   0.017   0.001   PHE C 175 
 TYR   0.015   0.002   TYR A 403 
 ARG   0.007   0.001   ARG B 487 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04890 (  490)
  hydrogen bonds       : angle       4.32002 ( 1374)
  metal coordination   : bond        0.00988 (   12)
  metal coordination   : angle       1.83713 (    9)
  covalent geometry    : bond        0.00481 (11471)
  covalent geometry    : angle       0.52562 (15629)

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

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

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 114
  time to evaluate  : 1.783 
Fit side-chains
   revert: symmetry clash
REVERT: A  141 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7720 (mmt90)
REVERT: B  148 GLU cc_start: 0.8080 (tt0) cc_final: 0.7525 (mt-10)
REVERT: C  389 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7676 (mpt-90)
  outliers start: 25
  outliers final: 20
  residues processed: 132
  average time/residue: 3.2994
  time to fit residues: 465.3865
Evaluate side-chains
  131 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 109
  time to evaluate  : 1.741 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   78 THR
Chi-restraints excluded: chain A residue  141 ARG
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  265 ARG
Chi-restraints excluded: chain A residue  317 ARG
Chi-restraints excluded: chain B residue   33 ARG
Chi-restraints excluded: chain B residue   36 GLU
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue   75 CYS
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  405 GLU
Chi-restraints excluded: chain B residue  444 ASP
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  148 SER
Chi-restraints excluded: chain C residue  151 VAL
Chi-restraints excluded: chain C residue  156 THR
Chi-restraints excluded: chain C residue  300 VAL
Chi-restraints excluded: chain C residue  301 SER
Chi-restraints excluded: chain C residue  389 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 106 optimal weight:    1.9990
   chunk 135 optimal weight:    9.9990
   chunk 123 optimal weight:    4.9990
   chunk 87 optimal weight:    1.9990
   chunk 66 optimal weight:    0.7980
   chunk 57 optimal weight:    1.9990
   chunk 92 optimal weight:    2.9990
   chunk 97 optimal weight:    0.7980
   chunk 1 optimal weight:    4.9990
   chunk 71 optimal weight:    2.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
A 195 ASN
B 330 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.106912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.082247 restraints weight = 39784.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.2898 rms_B_bonded: 1.76
r_work: 0.2791 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.2678 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.2678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8822
moved from start:          0.1056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  11483  Z= 0.163
  Angle     :  0.502   4.096  15638  Z= 0.264
  Chirality :  0.038   0.136   1765
  Planarity :  0.004   0.049   1918
  Dihedral  : 11.216  87.666   1891
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 1.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 16.32 %
    Favored  : 81.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.22), residues: 1345
  helix:  1.78 (0.23), residues: 534
  sheet: -0.51 (0.41), residues: 128
  loop : -0.15 (0.23), residues: 683

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 263 
 HIS   0.005   0.001   HIS B 174 
 PHE   0.015   0.001   PHE C 175 
 TYR   0.014   0.001   TYR A 403 
 ARG   0.007   0.000   ARG B 487 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04467 (  490)
  hydrogen bonds       : angle       4.24042 ( 1374)
  metal coordination   : bond        0.00566 (   12)
  metal coordination   : angle       1.77912 (    9)
  covalent geometry    : bond        0.00377 (11471)
  covalent geometry    : angle       0.50077 (15629)

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

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

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 112
  time to evaluate  : 1.711 
Fit side-chains
   revert: symmetry clash
REVERT: A  141 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7703 (mmt90)
REVERT: B  148 GLU cc_start: 0.8051 (tt0) cc_final: 0.7543 (mt-10)
REVERT: C  108 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8738 (tt)
REVERT: C  389 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.7686 (mpt-90)
  outliers start: 25
  outliers final: 18
  residues processed: 130
  average time/residue: 3.3373
  time to fit residues: 464.1769
Evaluate side-chains
  131 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 110
  time to evaluate  : 1.698 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   78 THR
Chi-restraints excluded: chain A residue  141 ARG
Chi-restraints excluded: chain A residue  155 GLN
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  265 ARG
Chi-restraints excluded: chain A residue  317 ARG
Chi-restraints excluded: chain B residue   33 ARG
Chi-restraints excluded: chain B residue   36 GLU
Chi-restraints excluded: chain B residue   75 CYS
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  405 GLU
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  148 SER
Chi-restraints excluded: chain C residue  151 VAL
Chi-restraints excluded: chain C residue  156 THR
Chi-restraints excluded: chain C residue  300 VAL
Chi-restraints excluded: chain C residue  301 SER
Chi-restraints excluded: chain C residue  389 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 13 optimal weight:    0.5980
   chunk 82 optimal weight:    0.6980
   chunk 91 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 67 optimal weight:    0.0980
   chunk 107 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 114 optimal weight:    0.0570
   chunk 5 optimal weight:    3.9990
   chunk 109 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.4498

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.110008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.085607 restraints weight = 38476.336|
|-----------------------------------------------------------------------------|
r_work (start): 0.2945 rms_B_bonded: 1.74
r_work: 0.2842 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.2730 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.2730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8778
moved from start:          0.1040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  11483  Z= 0.087
  Angle     :  0.456   5.081  15638  Z= 0.237
  Chirality :  0.037   0.135   1765
  Planarity :  0.004   0.061   1918
  Dihedral  : 11.013  86.220   1891
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 1.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 17.87 %
    Favored  : 80.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.27 (0.23), residues: 1345
  helix:  2.20 (0.23), residues: 527
  sheet: -0.16 (0.40), residues: 148
  loop :  0.04 (0.24), residues: 670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 239 
 HIS   0.004   0.001   HIS A 367 
 PHE   0.008   0.001   PHE C 175 
 TYR   0.010   0.001   TYR A 403 
 ARG   0.008   0.000   ARG B 487 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03419 (  490)
  hydrogen bonds       : angle       3.97982 ( 1374)
  metal coordination   : bond        0.00326 (   12)
  metal coordination   : angle       1.40556 (    9)
  covalent geometry    : bond        0.00197 (11471)
  covalent geometry    : angle       0.45469 (15629)

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

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

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 116
  time to evaluate  : 4.020 
Fit side-chains
REVERT: A   92 VAL cc_start: 0.7844 (p) cc_final: 0.7629 (m)
REVERT: B   84 ARG cc_start: 0.7502 (ttp-110) cc_final: 0.7284 (ttp-110)
REVERT: B  148 GLU cc_start: 0.8031 (tt0) cc_final: 0.7512 (mt-10)
REVERT: C   83 ARG cc_start: 0.7513 (ttp-110) cc_final: 0.7236 (mtm-85)
REVERT: C  108 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8714 (tt)
  outliers start: 14
  outliers final: 9
  residues processed: 126
  average time/residue: 4.3173
  time to fit residues: 585.8611
Evaluate side-chains
  121 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 111
  time to evaluate  : 1.675 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 THR
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  265 ARG
Chi-restraints excluded: chain B residue   33 ARG
Chi-restraints excluded: chain B residue   75 CYS
Chi-restraints excluded: chain B residue  180 SER
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  151 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 115 optimal weight:    1.9990
   chunk 93 optimal weight:    2.9990
   chunk 44 optimal weight:    0.2980
   chunk 21 optimal weight:    0.6980
   chunk 101 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   chunk 121 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 133 optimal weight:    2.9990
   chunk 135 optimal weight:    9.9990
   overall best weight:    0.9582

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.108993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.084363 restraints weight = 39501.668|
|-----------------------------------------------------------------------------|
r_work (start): 0.2926 rms_B_bonded: 1.77
r_work: 0.2822 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.2710 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.2710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8799
moved from start:          0.1025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  11483  Z= 0.119
  Angle     :  0.471   5.377  15638  Z= 0.245
  Chirality :  0.037   0.136   1765
  Planarity :  0.004   0.058   1918
  Dihedral  : 10.922  87.103   1888
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 1.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 18.04 %
    Favored  : 80.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.23), residues: 1345
  helix:  2.02 (0.23), residues: 540
  sheet: -0.17 (0.40), residues: 148
  loop :  0.02 (0.24), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 263 
 HIS   0.004   0.001   HIS B 174 
 PHE   0.013   0.001   PHE C 175 
 TYR   0.013   0.001   TYR A 403 
 ARG   0.008   0.000   ARG B 487 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03832 (  490)
  hydrogen bonds       : angle       4.02700 ( 1374)
  metal coordination   : bond        0.00397 (   12)
  metal coordination   : angle       1.49350 (    9)
  covalent geometry    : bond        0.00275 (11471)
  covalent geometry    : angle       0.46980 (15629)

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

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

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 112
  time to evaluate  : 1.847 
Fit side-chains
   revert: symmetry clash
REVERT: A  141 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7681 (mmt90)
REVERT: B   84 ARG cc_start: 0.7486 (ttp-110) cc_final: 0.7270 (ttp-110)
REVERT: B  148 GLU cc_start: 0.8028 (tt0) cc_final: 0.7518 (mt-10)
REVERT: C   83 ARG cc_start: 0.7498 (ttp-110) cc_final: 0.7225 (mtm-85)
REVERT: C  108 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8736 (tt)
REVERT: C  110 ASP cc_start: 0.7096 (m-30) cc_final: 0.6836 (m-30)
  outliers start: 14
  outliers final: 10
  residues processed: 121
  average time/residue: 3.5080
  time to fit residues: 454.7586
Evaluate side-chains
  125 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 113
  time to evaluate  : 2.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 THR
Chi-restraints excluded: chain A residue  141 ARG
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  265 ARG
Chi-restraints excluded: chain A residue  317 ARG
Chi-restraints excluded: chain B residue   33 ARG
Chi-restraints excluded: chain B residue   75 CYS
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  180 SER
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue  108 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 47 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 53 optimal weight:    3.9990
   chunk 119 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 64 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 40 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    1.0984

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.108541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.083904 restraints weight = 39517.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.2919 rms_B_bonded: 1.77
r_work: 0.2815 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.2703 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.2703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8804
moved from start:          0.1070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  11483  Z= 0.129
  Angle     :  0.481   5.981  15638  Z= 0.251
  Chirality :  0.037   0.136   1765
  Planarity :  0.004   0.061   1918
  Dihedral  : 10.949  88.287   1887
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 1.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 18.21 %
    Favored  : 80.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.23), residues: 1345
  helix:  2.01 (0.23), residues: 534
  sheet: -0.20 (0.40), residues: 148
  loop : -0.03 (0.23), residues: 663

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 209 
 HIS   0.004   0.001   HIS B 174 
 PHE   0.014   0.001   PHE C 175 
 TYR   0.013   0.001   TYR A 403 
 ARG   0.009   0.000   ARG B 487 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04008 (  490)
  hydrogen bonds       : angle       4.06580 ( 1374)
  metal coordination   : bond        0.00441 (   12)
  metal coordination   : angle       1.59522 (    9)
  covalent geometry    : bond        0.00298 (11471)
  covalent geometry    : angle       0.47944 (15629)

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

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

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 112
  time to evaluate  : 2.166 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 VAL cc_start: 0.7864 (p) cc_final: 0.7643 (m)
REVERT: A  141 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7663 (mmt90)
REVERT: B  148 GLU cc_start: 0.8048 (tt0) cc_final: 0.7546 (mt-10)
REVERT: C   83 ARG cc_start: 0.7478 (ttp-110) cc_final: 0.7210 (mtm-85)
REVERT: C  108 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8757 (tt)
REVERT: C  110 ASP cc_start: 0.7116 (m-30) cc_final: 0.6825 (m-30)
  outliers start: 12
  outliers final: 10
  residues processed: 120
  average time/residue: 4.6739
  time to fit residues: 607.3938
Evaluate side-chains
  122 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 110
  time to evaluate  : 2.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 THR
Chi-restraints excluded: chain A residue  141 ARG
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  265 ARG
Chi-restraints excluded: chain A residue  317 ARG
Chi-restraints excluded: chain B residue   33 ARG
Chi-restraints excluded: chain B residue   75 CYS
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  180 SER
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  151 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 67 optimal weight:    0.8980
   chunk 115 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 28 optimal weight:    0.1980
   chunk 89 optimal weight:    2.9990
   chunk 127 optimal weight:    3.9990
   chunk 82 optimal weight:    0.9980
   chunk 131 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 125 optimal weight:    1.9990
   overall best weight:    0.7180

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.109478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.084847 restraints weight = 39711.735|
|-----------------------------------------------------------------------------|
r_work (start): 0.2934 rms_B_bonded: 1.77
r_work: 0.2830 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.2718 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.2718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8791
moved from start:          0.1068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  11483  Z= 0.103
  Angle     :  0.464   6.140  15638  Z= 0.240
  Chirality :  0.037   0.136   1765
  Planarity :  0.004   0.064   1918
  Dihedral  : 10.870  87.206   1886
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 1.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 18.38 %
    Favored  : 80.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.23), residues: 1345
  helix:  2.08 (0.23), residues: 535
  sheet: -0.19 (0.40), residues: 148
  loop :  0.01 (0.23), residues: 662

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 209 
 HIS   0.004   0.001   HIS B 174 
 PHE   0.011   0.001   PHE C 175 
 TYR   0.012   0.001   TYR A 403 
 ARG   0.009   0.000   ARG B 487 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03637 (  490)
  hydrogen bonds       : angle       3.97794 ( 1374)
  metal coordination   : bond        0.00314 (   12)
  metal coordination   : angle       1.43053 (    9)
  covalent geometry    : bond        0.00237 (11471)
  covalent geometry    : angle       0.46255 (15629)

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

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

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 112
  time to evaluate  : 1.620 
Fit side-chains
REVERT: A   92 VAL cc_start: 0.7822 (p) cc_final: 0.7616 (m)
REVERT: B  148 GLU cc_start: 0.8043 (tt0) cc_final: 0.7568 (mt-10)
REVERT: C  110 ASP cc_start: 0.7085 (m-30) cc_final: 0.6830 (m-30)
REVERT: C  111 ARG cc_start: 0.5509 (ptp90) cc_final: 0.5307 (ptp90)
  outliers start: 12
  outliers final: 10
  residues processed: 120
  average time/residue: 3.3608
  time to fit residues: 430.4050
Evaluate side-chains
  122 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 112
  time to evaluate  : 1.729 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 THR
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  265 ARG
Chi-restraints excluded: chain B residue   33 ARG
Chi-restraints excluded: chain B residue   75 CYS
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  180 SER
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue  148 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 122 optimal weight:    2.9990
   chunk 125 optimal weight:    0.6980
   chunk 35 optimal weight:    2.9990
   chunk 134 optimal weight:    3.9990
   chunk 84 optimal weight:    1.9990
   chunk 130 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 117 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 195 ASN
B 330 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.108062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.083374 restraints weight = 39748.306|
|-----------------------------------------------------------------------------|
r_work (start): 0.2910 rms_B_bonded: 1.77
r_work: 0.2807 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.2695 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.2695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8811
moved from start:          0.1124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  11483  Z= 0.149
  Angle     :  0.491   4.954  15638  Z= 0.257
  Chirality :  0.038   0.136   1765
  Planarity :  0.004   0.060   1918
  Dihedral  : 10.952  88.309   1886
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 1.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 17.70 %
    Favored  : 80.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.06 (0.23), residues: 1345
  helix:  1.95 (0.23), residues: 534
  sheet: -0.24 (0.40), residues: 148
  loop : -0.04 (0.23), residues: 663

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B   2 
 HIS   0.005   0.001   HIS B 174 
 PHE   0.015   0.001   PHE C 175 
 TYR   0.014   0.001   TYR A 403 
 ARG   0.008   0.000   ARG B 487 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04194 (  490)
  hydrogen bonds       : angle       4.10329 ( 1374)
  metal coordination   : bond        0.00549 (   12)
  metal coordination   : angle       1.65309 (    9)
  covalent geometry    : bond        0.00348 (11471)
  covalent geometry    : angle       0.48910 (15629)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 15565.87 seconds
wall clock time: 268 minutes 18.93 seconds (16098.93 seconds total)