Starting phenix.real_space_refine
on Sun Aug 24 15:01:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pt6_17868/08_2025/8pt6_17868_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pt6_17868/08_2025/8pt6_17868.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.03
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pt6_17868/08_2025/8pt6_17868_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pt6_17868/08_2025/8pt6_17868_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pt6_17868/08_2025/8pt6_17868.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pt6_17868/08_2025/8pt6_17868.map"
  }
  resolution = 3.03
  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=   0.001
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: 8
    Type Number    sf(0)   Gaussians
     Zn      3      6.06       5
     P      31      5.49       5
     Mg      2      5.21       5
     S      63      5.16       5
     C    6433      2.51       5
     N    1828      2.21       5
     O    2025      1.98       5
     H   10051      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 20436
  Number of models: 1
  Model: ""
    Number of chains: 10
    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: 7971
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 515, 7970
          Classifications: {'peptide': 515}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 493}
      Conformer: "B"
        Number of residues, atoms: 515, 7970
          Classifications: {'peptide': 515}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 493}
          bond proxies already assigned to first conformer: 8041
    Chain: "C"
      Number of atoms: 4887
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 310, 4887
          Classifications: {'peptide': 310}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 17, 'TRANS': 292}
          Chain breaks: 1
    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': 2, 'rna3p_pur': 2, 'rna3p_pyr': 7}
          Link IDs: {'rna2p': 4, 'rna3p': 8}
    Chain: "S"
      Number of atoms: 486
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 486
          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: "F"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 29
          Unusual residues: {'CTP': 1}
          Classifications: {'undetermined': 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: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 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: "F"
      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   2585  SG  CYS A 161      44.562  50.821  17.982  1.00 61.93           S
  ATOM   4473  SG  CYS A 282      42.322  48.732  15.482  1.00 64.89           S
  ATOM  16942  SG  CYS C 146      29.762  69.730  80.614  1.00127.37           S
  ATOM  17130  SG  CYS C 159      31.471  69.008  77.299  1.00111.13           S
  ATOM  17185  SG  CYS C 163      32.787  71.906  79.371  1.00119.08           S
  ATOM  17195  SG  CYS C 164      33.107  68.366  80.746  1.00108.45           S
  ATOM  18275  SG  CYS C 233      36.504  91.333  70.828  1.00139.04           S
  ATOM  18300  SG  CYS C 235      37.665  88.886  73.425  1.00130.85           S

  Time building chain proxies: 5.05, per 1000 atoms: 0.25
  Number of scatterers: 20436
  At special positions: 0
  Unit cell: (89.04, 114.24, 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      3     29.99
     S      63     16.00
     P      31     15.00
     Mg      2     11.99
     O    2025      8.00
     N    1828      7.00
     C    6433      6.00
     H   10051      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: 1.99
  Conformation dependent library (CDL) restraints added in 690.9 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 501 "
        pdb="ZN    ZN A 501 " - pdb=" NE2 HIS A 296 "
        pdb="ZN    ZN A 501 " - pdb=" ND1 HIS A 284 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 282 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 161 "
      pdb="  ZN C 501 "
        pdb="ZN    ZN C 501 " - pdb=" SG  CYS C 159 "
        pdb="ZN    ZN C 501 " - pdb=" SG  CYS C 146 "
        pdb="ZN    ZN C 501 " - pdb=" SG  CYS C 163 "
        pdb="ZN    ZN C 501 " - pdb=" SG  CYS C 164 "
      pdb="  ZN C 502 "
        pdb="ZN    ZN C 502 " - pdb=" NE2 HIS C 191 "
        pdb="ZN    ZN C 502 " - pdb=" ND1 HIS C 184 "
        pdb="ZN    ZN C 502 " - pdb=" SG  CYS C 235 "
        pdb="ZN    ZN C 502 " - pdb=" SG  CYS C 233 "
      Number of angles added : 8


  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2336

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 12 sheets defined
      41.5% alpha, 13.9% beta
      7 base pairs and 8 stacking pairs defined.
    Time for finding SS restraints: 4.28
  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 11
    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: 3.622A  pdb=" N   ILE A 145 " --> pdb=" O   ARG A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 169
      removed outlier: 3.627A  pdb=" N   GLY A 168 " --> pdb=" O   LEU A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 189
    Processing helix  chain 'A' and resid 223 through 235
      removed outlier: 3.690A  pdb=" N   THR A 235 " --> pdb=" O   ILE A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 301 through 310
    Processing helix  chain 'A' and resid 312 through 323
      removed outlier: 4.242A  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: 3.905A  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: 3.611A  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 65 through 70
      removed outlier: 3.831A  pdb=" N   LEU B  69 " --> pdb=" O   VAL B  65 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   TYR B  70 " --> pdb=" O   ASP B  66 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 65 through 70'
    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
    Processing helix  chain 'B' and resid 184 through 187
      removed outlier: 3.619A  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 204
    Processing helix  chain 'B' and resid 216 through 221
      removed outlier: 3.571A  pdb=" N   ILE B 221 " --> pdb=" O   TYR B 217 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 233
    Processing helix  chain 'B' and resid 235 through 248
      removed outlier: 3.750A  pdb=" N   GLY B 239 " --> pdb=" O   MET B 235 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   VAL B 240 " --> pdb=" O   GLY B 236 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 270 through 279
      removed outlier: 3.849A  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: 3.556A  pdb=" N   GLY B 413 " --> pdb=" O   THR B 410 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 419 through 426
    Processing helix  chain 'B' and resid 429 through 436
      removed outlier: 3.925A  pdb=" N   GLN B 434 " --> pdb=" O   PHE B 431 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 442 through 454
      removed outlier: 3.673A  pdb=" N   LYS B 454 " --> pdb=" O   VAL B 450 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 479 through 497
      removed outlier: 3.650A  pdb=" N   LEU B 497 " --> pdb=" O   HIS B 493 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 514
    Processing helix  chain 'C' and resid 2 through 8
    Processing helix  chain 'C' and resid 16 through 22
      removed outlier: 3.553A  pdb=" N   HIS C  22 " --> pdb=" O   GLU C  18 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 33 through 40
    Processing helix  chain 'C' and resid 42 through 55
    Processing helix  chain 'C' and resid 56 through 59
      removed outlier: 3.509A  pdb=" N   LEU C  59 " --> pdb=" O   LEU C  56 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 56 through 59'
    Processing helix  chain 'C' and resid 87 through 98
    Processing helix  chain 'C' and resid 100 through 107
    Processing helix  chain 'C' and resid 147 through 152
    Processing helix  chain 'C' and resid 208 through 219
    Processing helix  chain 'C' and resid 234 through 241
    Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 27
      removed outlier: 6.247A  pdb=" N   TRP A  52 " --> pdb=" O   VAL A  69 " (cutoff:3.500A)
      removed outlier: 7.227A  pdb=" N   CYS A  71 " --> pdb=" O   TRP A  52 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   ALA A  54 " --> pdb=" O   CYS A  71 " (cutoff:3.500A)
      removed outlier: 7.273A  pdb=" N   LEU A  73 " --> pdb=" O   ALA A  54 " (cutoff:3.500A)
      removed outlier: 7.042A  pdb=" N   GLU A  56 " --> pdb=" O   LEU A  73 " (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: 6.297A  pdb=" N   TRP A 198 " --> pdb=" O   ALA A 251 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 192 through 194
      removed outlier: 6.297A  pdb=" N   TRP A 198 " --> pdb=" O   ALA A 251 " (cutoff:3.500A)
      removed outlier: 6.949A  pdb=" N   SER A 248 " --> pdb=" O   LEU A 277 " (cutoff:3.500A)
      removed outlier: 4.462A  pdb=" N   LEU A 277 " --> pdb=" O   SER A 248 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   HIS A 271 " --> pdb=" O   VAL A 254 " (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: 3.666A  pdb=" N   ARG B 155 " --> pdb=" O   ARG B 145 " (cutoff:3.500A)
      removed outlier: 7.058A  pdb=" N   PHE B 140 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 326 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 72 through 83
      removed outlier: 7.110A  pdb=" N   LYS C  75 " --> pdb=" O   TYR C 119 " (cutoff:3.500A)
      removed outlier: 5.071A  pdb=" N   TYR C 119 " --> pdb=" O   LYS C  75 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 221 through 224
      removed outlier: 3.856A  pdb=" N   CYS C 259 " --> pdb=" O   GLY C 262 " (cutoff:3.500A)
      removed outlier: 6.147A  pdb=" N   VAL C 264 " --> pdb=" O   ALA C 257 " (cutoff:3.500A)
      removed outlier: 6.053A  pdb=" N   ALA C 257 " --> pdb=" O   VAL C 264 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 385 through 386
      removed outlier: 3.795A  pdb=" N   ALA C 414 " --> pdb=" O   CYS C 409 " (cutoff:3.500A)

    431 hydrogen bonds defined for protein.
    1185 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      17 hydrogen bonds
      34 hydrogen bond angles
      0 basepair planarities
      7 basepair parallelities
      8 stacking parallelities
  Total time for adding SS restraints: 4.90

  Time building geometry restraints manager: 2.65 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: 10019
        1.03 -     1.23: 44
        1.23 -     1.42: 4497
        1.42 -     1.62: 6061
        1.62 -     1.81: 87
  Bond restraints: 20708
  Sorted by residual:
  bond pdb=" C5  CTP F   1 "
       pdb=" C6  CTP F   1 "
    ideal  model  delta    sigma   weight residual
    1.390  1.342  0.048 2.00e-02 2.50e+03 5.72e+00
  bond pdb=" C4' CTP F   1 "
       pdb=" O4' CTP F   1 "
    ideal  model  delta    sigma   weight residual
    1.410  1.452 -0.042 2.00e-02 2.50e+03 4.33e+00
  bond pdb=" C5' CTP F   1 "
       pdb=" O5' CTP F   1 "
    ideal  model  delta    sigma   weight residual
    1.410  1.451 -0.041 2.00e-02 2.50e+03 4.14e+00
  bond pdb=" C4  CTP F   1 "
       pdb=" N3  CTP F   1 "
    ideal  model  delta    sigma   weight residual
    1.380  1.340  0.040 2.00e-02 2.50e+03 4.02e+00
  bond pdb=" C4  CTP F   1 "
       pdb=" C5  CTP F   1 "
    ideal  model  delta    sigma   weight residual
    1.390  1.421 -0.031 2.00e-02 2.50e+03 2.39e+00
  ... (remaining 20703 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.80: 37305
        2.80 -     5.61: 85
        5.61 -     8.41: 2
        8.41 -    11.22: 2
       11.22 -    14.02: 3
  Bond angle restraints: 37397
  Sorted by residual:
  angle pdb=" PA  CTP F   1 "
        pdb=" O3A CTP F   1 "
        pdb=" PB  CTP F   1 "
      ideal   model   delta    sigma   weight residual
     120.50  134.52  -14.02 3.00e+00 1.11e-01 2.19e+01
  angle pdb=" PB  CTP F   1 "
        pdb=" O3B CTP F   1 "
        pdb=" PG  CTP F   1 "
      ideal   model   delta    sigma   weight residual
     120.50  131.79  -11.29 3.00e+00 1.11e-01 1.42e+01
  angle pdb=" C2' CTP F   1 "
        pdb=" C3' CTP F   1 "
        pdb=" C4' CTP F   1 "
      ideal   model   delta    sigma   weight residual
     111.00   99.78   11.22 3.00e+00 1.11e-01 1.40e+01
  angle pdb=" C1' CTP F   1 "
        pdb=" C2' CTP F   1 "
        pdb=" C3' CTP F   1 "
      ideal   model   delta    sigma   weight residual
     111.00   99.91   11.09 3.00e+00 1.11e-01 1.37e+01
  angle pdb=" O1B CTP F   1 "
        pdb=" PB  CTP F   1 "
        pdb=" O2B CTP F   1 "
      ideal   model   delta    sigma   weight residual
     109.50  119.32   -9.82 3.00e+00 1.11e-01 1.07e+01
  ... (remaining 37392 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.28: 9343
       35.28 -    70.56: 413
       70.56 -   105.84: 19
      105.84 -   141.11: 1
      141.11 -   176.39: 2
  Dihedral angle restraints: 9778
    sinusoidal: 5559
      harmonic: 4219
  Sorted by residual:
  dihedral pdb=" O3B CTP F   1 "
           pdb=" O3A CTP F   1 "
           pdb=" PB  CTP F   1 "
           pdb=" PA  CTP F   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     320.71  166.48  154.22     1      2.00e+01 2.50e-03 4.56e+01
  dihedral pdb=" O1G CTP F   1 "
           pdb=" O3B CTP F   1 "
           pdb=" PG  CTP F   1 "
           pdb=" PB  CTP F   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
      82.72 -169.86 -107.42     1      2.00e+01 2.50e-03 3.12e+01
  dihedral pdb=" O3A CTP F   1 "
           pdb=" O3B CTP F   1 "
           pdb=" PB  CTP F   1 "
           pdb=" PG  CTP F   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -155.50  -52.04 -103.46     1      2.00e+01 2.50e-03 2.96e+01
  ... (remaining 9775 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1440
       0.051 -    0.102: 154
       0.102 -    0.153: 40
       0.153 -    0.204: 0
       0.204 -    0.255: 1
  Chirality restraints: 1635
  Sorted by residual:
  chirality pdb=" C2' CTP F   1 "
            pdb=" C1' CTP F   1 "
            pdb=" C3' CTP F   1 "
            pdb=" O2' CTP F   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47   -2.73    0.25 2.00e-01 2.50e+01 1.62e+00
  chirality pdb=" C3'   G S   1 "
            pdb=" C4'   G S   1 "
            pdb=" O3'   G S   1 "
            pdb=" C2'   G S   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.60   -0.15 2.00e-01 2.50e+01 5.51e-01
  chirality pdb=" C3' CTP F   1 "
            pdb=" C2' CTP F   1 "
            pdb=" C4' CTP F   1 "
            pdb=" O3' CTP F   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47   -2.61    0.14 2.00e-01 2.50e+01 4.69e-01
  ... (remaining 1632 not shown)

  Planarity restraints: 2962
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS B 161 "   -0.034 5.00e-02 4.00e+02   5.09e-02 4.14e+00
        pdb=" N   PRO B 162 "    0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO B 162 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO B 162 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A S   8 "    0.019 2.00e-02 2.50e+03   8.45e-03 2.32e+00
        pdb=" N9    A S   8 "   -0.023 2.00e-02 2.50e+03
        pdb=" C8    A S   8 "   -0.001 2.00e-02 2.50e+03
        pdb=" N7    A S   8 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    A S   8 "    0.000 2.00e-02 2.50e+03
        pdb=" C6    A S   8 "    0.002 2.00e-02 2.50e+03
        pdb=" N6    A S   8 "    0.004 2.00e-02 2.50e+03
        pdb=" N1    A S   8 "    0.002 2.00e-02 2.50e+03
        pdb=" C2    A S   8 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    A S   8 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4    A S   8 "    0.000 2.00e-02 2.50e+03
        pdb=" H8    A S   8 "   -0.000 2.00e-02 2.50e+03
        pdb=" H2    A S   8 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 469 "    0.023 5.00e-02 4.00e+02   3.46e-02 1.92e+00
        pdb=" N   PRO B 470 "   -0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO B 470 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 470 "    0.019 5.00e-02 4.00e+02
  ... (remaining 2959 not shown)

  Histogram of nonbonded interaction distances:
        1.00 -     1.72: 25
        1.72 -     2.44: 11247
        2.44 -     3.16: 62150
        3.16 -     3.88: 84118
        3.88 -     4.60: 133872
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 291412
  Sorted by model distance:
  nonbonded pdb=" HD2 HIS C 266 "
            pdb="HG13 VAL C 269 "
     model   vdw
     0.997 2.270
  nonbonded pdb=" HB2 CYS C 233 "
            pdb="ZN    ZN C 502 "
     model   vdw
     1.374 1.544
  nonbonded pdb=" OE1 GLU C  89 "
            pdb=" H   GLU C  89 "
     model   vdw
     1.484 2.450
  nonbonded pdb=" O   GLY A 309 "
            pdb="HH22 ARG B 394 "
     model   vdw
     1.559 2.450
  nonbonded pdb=" OD2 ASP A  43 "
            pdb=" H   PHE A  55 "
     model   vdw
     1.574 2.450
  ... (remaining 291407 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.40 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:             1.770
  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:             0.130
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     29.990
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  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:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8405
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      :  0.003   0.061  10669  Z= 0.117
  Angle     :  0.556  14.024  14545  Z= 0.271
  Chirality :  0.037   0.255   1635
  Planarity :  0.003   0.051   1766
  Dihedral  : 18.464 176.392   4163
  Min Nonbonded Distance : 1.826

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.73 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 25.02 %
    Favored  : 72.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.06 (0.25), residues: 1234
  helix:  1.99 (0.25), residues: 477
  sheet:  0.43 (0.42), residues: 150
  loop : -0.22 (0.26), residues: 607

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 475 
 TYR   0.009   0.001   TYR A 403 
 PHE   0.010   0.001   PHE C  44 
 TRP   0.005   0.001   TRP C 183 
 HIS   0.002   0.001   HIS A 371 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 (10657)
  covalent geometry    : angle       0.54648 (14537)
  hydrogen bonds       : bond        0.11653 (  441)
  hydrogen bonds       : angle       5.41971 ( 1219)
  metal coordination   : bond        0.01863 (   12)
  metal coordination   : angle       4.46542 (    8)

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

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

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 91
  time to evaluate  : 0.588 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  204 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7725 (pm20)
REVERT: B  219 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.7781 (mp0)
  outliers start: 26
  outliers final: 23
  residues processed: 115
  average time/residue: 0.3001
  time to fit residues: 46.5178
Evaluate side-chains
  112 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 87
  time to evaluate  : 0.581 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 CYS
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  340 SER
Chi-restraints excluded: chain B residue   15 SER
Chi-restraints excluded: chain B residue   19 SER
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   75 CYS
Chi-restraints excluded: chain B residue  204 GLU
Chi-restraints excluded: chain B residue  219 GLU
Chi-restraints excluded: chain B residue  289 ASP
Chi-restraints excluded: chain B residue  326 SER
Chi-restraints excluded: chain B residue  337 ASP
Chi-restraints excluded: chain B residue  367 SER
Chi-restraints excluded: chain B residue  475 ARG
Chi-restraints excluded: chain B residue  484 SER
Chi-restraints excluded: chain B residue  503 THR
Chi-restraints excluded: chain C residue   17 THR
Chi-restraints excluded: chain C residue   41 SER
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue  115 GLU
Chi-restraints excluded: chain C residue  125 ASP
Chi-restraints excluded: chain C residue  146 CYS
Chi-restraints excluded: chain C residue  238 VAL
Chi-restraints excluded: chain C residue  269 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 113 optimal weight:   10.0000
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    1.9990
   chunk 123 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   overall best weight:    1.3586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.148722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.103070 restraints weight = 41951.921|
|-----------------------------------------------------------------------------|
r_work (start): 0.3174 rms_B_bonded: 2.34
r_work: 0.3053 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2938 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2941
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2941 r_free = 0.2941    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2941 r_free = 0.2941    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2941
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8494
moved from start:          0.0656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  10669  Z= 0.161
  Angle     :  0.525   8.687  14545  Z= 0.268
  Chirality :  0.038   0.150   1635
  Planarity :  0.004   0.054   1766
  Dihedral  : 13.610 176.108   1829
  Min Nonbonded Distance : 1.725

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.05 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 22.97 %
    Favored  : 74.04 %
  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:  0.95 (0.24), residues: 1234
  helix:  1.86 (0.24), residues: 478
  sheet:  0.56 (0.42), residues: 142
  loop : -0.30 (0.26), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  73 
 TYR   0.014   0.001   TYR A 403 
 PHE   0.014   0.001   PHE C  44 
 TRP   0.009   0.001   TRP A 346 
 HIS   0.005   0.001   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 (10657)
  covalent geometry    : angle       0.51729 (14537)
  hydrogen bonds       : bond        0.04406 (  441)
  hydrogen bonds       : angle       4.57330 ( 1219)
  metal coordination   : bond        0.02114 (   12)
  metal coordination   : angle       3.81004 (    8)

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

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

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 84
  time to evaluate  : 0.498 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  121 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8556 (mp)
REVERT: B  219 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8103 (mt-10)
REVERT: B  222 ASP cc_start: 0.8524 (OUTLIER) cc_final: 0.8134 (t70)
  outliers start: 32
  outliers final: 17
  residues processed: 112
  average time/residue: 0.2862
  time to fit residues: 43.0250
Evaluate side-chains
  104 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 84
  time to evaluate  : 0.541 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 CYS
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   75 CYS
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  219 GLU
Chi-restraints excluded: chain B residue  222 ASP
Chi-restraints excluded: chain B residue  289 ASP
Chi-restraints excluded: chain B residue  337 ASP
Chi-restraints excluded: chain B residue  367 SER
Chi-restraints excluded: chain B residue  475 ARG
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  496 SER
Chi-restraints excluded: chain B residue  503 THR
Chi-restraints excluded: chain C residue   16 ILE
Chi-restraints excluded: chain C residue   55 ASP
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue  238 VAL
Chi-restraints excluded: chain C residue  269 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 71 optimal weight:    0.5980
   chunk 16 optimal weight:    2.9990
   chunk 3 optimal weight:    6.9990
   chunk 67 optimal weight:    1.9990
   chunk 98 optimal weight:    0.6980
   chunk 110 optimal weight:    6.9990
   chunk 94 optimal weight:    0.7980
   chunk 116 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   overall best weight:    0.8184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.149751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.104192 restraints weight = 41587.345|
|-----------------------------------------------------------------------------|
r_work (start): 0.3194 rms_B_bonded: 2.39
r_work: 0.3071 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2957 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2961
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2961 r_free = 0.2961    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2961 r_free = 0.2961    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2961
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
moved from start:          0.0853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068  10669  Z= 0.115
  Angle     :  0.484   9.102  14545  Z= 0.245
  Chirality :  0.037   0.137   1635
  Planarity :  0.004   0.052   1766
  Dihedral  : 13.146 170.294   1811
  Min Nonbonded Distance : 1.740

Molprobity Statistics.
  All-atom Clashscore : 2.79
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.57 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 23.16 %
    Favored  : 74.88 %
  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:  1.04 (0.24), residues: 1234
  helix:  1.98 (0.24), residues: 478
  sheet:  0.54 (0.43), residues: 144
  loop : -0.28 (0.26), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 155 
 TYR   0.012   0.001   TYR A 403 
 PHE   0.011   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        0.00259 (10657)
  covalent geometry    : angle       0.47632 (14537)
  hydrogen bonds       : bond        0.03871 (  441)
  hydrogen bonds       : angle       4.29278 ( 1219)
  metal coordination   : bond        0.02130 (   12)
  metal coordination   : angle       3.71428 (    8)

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

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

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 87
  time to evaluate  : 0.564 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  147 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8406 (mppt)
REVERT: B   33 ARG cc_start: 0.8117 (mtp180) cc_final: 0.7845 (mtp180)
REVERT: B  121 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8541 (mp)
  outliers start: 21
  outliers final: 15
  residues processed: 105
  average time/residue: 0.3077
  time to fit residues: 42.6543
Evaluate side-chains
  102 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 85
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 CYS
Chi-restraints excluded: chain A residue  147 LYS
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain A residue  269 SER
Chi-restraints excluded: chain B residue   75 CYS
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  219 GLU
Chi-restraints excluded: chain B residue  289 ASP
Chi-restraints excluded: chain B residue  302 ARG
Chi-restraints excluded: chain B residue  475 ARG
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  496 SER
Chi-restraints excluded: chain B residue  503 THR
Chi-restraints excluded: chain C residue   16 ILE
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue  269 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 86 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 72 optimal weight:    0.8980
   chunk 120 optimal weight:    6.9990
   chunk 33 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 41 optimal weight:    0.5980
   chunk 44 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   overall best weight:    1.0782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.148748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.102170 restraints weight = 41612.768|
|-----------------------------------------------------------------------------|
r_work (start): 0.3160 rms_B_bonded: 2.17
r_work: 0.3048 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2931 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2937
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2937 r_free = 0.2937    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2937 r_free = 0.2937    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2937
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8482
moved from start:          0.0997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066  10669  Z= 0.135
  Angle     :  0.493   9.007  14545  Z= 0.250
  Chirality :  0.037   0.137   1635
  Planarity :  0.004   0.053   1766
  Dihedral  : 13.088 166.684   1805
  Min Nonbonded Distance : 1.724

Molprobity Statistics.
  All-atom Clashscore : 2.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 22.13 %
    Favored  : 75.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.98 (0.24), residues: 1234
  helix:  1.92 (0.24), residues: 478
  sheet:  0.49 (0.43), residues: 144
  loop : -0.30 (0.26), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 155 
 TYR   0.013   0.001   TYR A 403 
 PHE   0.013   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        0.00306 (10657)
  covalent geometry    : angle       0.48527 (14537)
  hydrogen bonds       : bond        0.03927 (  441)
  hydrogen bonds       : angle       4.26523 ( 1219)
  metal coordination   : bond        0.02150 (   12)
  metal coordination   : angle       3.62174 (    8)

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

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

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 85
  time to evaluate  : 0.574 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  147 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8376 (mppt)
REVERT: B   33 ARG cc_start: 0.8120 (mtp180) cc_final: 0.7761 (mtp180)
REVERT: B  121 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8551 (mp)
REVERT: B  127 ASP cc_start: 0.8033 (m-30) cc_final: 0.7757 (m-30)
REVERT: B  219 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.7699 (mt-10)
REVERT: B  222 ASP cc_start: 0.8495 (OUTLIER) cc_final: 0.8076 (t70)
  outliers start: 24
  outliers final: 19
  residues processed: 106
  average time/residue: 0.3273
  time to fit residues: 45.9659
Evaluate side-chains
  107 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 84
  time to evaluate  : 0.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 CYS
Chi-restraints excluded: chain A residue  147 LYS
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain A residue  269 SER
Chi-restraints excluded: chain B residue   75 CYS
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  211 ASN
Chi-restraints excluded: chain B residue  219 GLU
Chi-restraints excluded: chain B residue  222 ASP
Chi-restraints excluded: chain B residue  289 ASP
Chi-restraints excluded: chain B residue  302 ARG
Chi-restraints excluded: chain B residue  475 ARG
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  496 SER
Chi-restraints excluded: chain B residue  503 THR
Chi-restraints excluded: chain C residue    6 LYS
Chi-restraints excluded: chain C residue   16 ILE
Chi-restraints excluded: chain C residue   55 ASP
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue  115 GLU
Chi-restraints excluded: chain C residue  269 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 123 optimal weight:    3.9990
   chunk 5 optimal weight:    9.9990
   chunk 28 optimal weight:    0.6980
   chunk 43 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.7782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.149345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.104363 restraints weight = 41483.433|
|-----------------------------------------------------------------------------|
r_work (start): 0.3191 rms_B_bonded: 2.28
r_work: 0.3068 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2954 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2957
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2957 r_free = 0.2957    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2957 r_free = 0.2957    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2957
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8465
moved from start:          0.1121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068  10669  Z= 0.110
  Angle     :  0.477   9.048  14545  Z= 0.242
  Chirality :  0.037   0.139   1635
  Planarity :  0.004   0.051   1766
  Dihedral  : 12.958 166.210   1805
  Min Nonbonded Distance : 1.755

Molprobity Statistics.
  All-atom Clashscore : 2.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 22.13 %
    Favored  : 75.54 %
  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:  1.05 (0.24), residues: 1234
  helix:  2.02 (0.24), residues: 478
  sheet:  0.40 (0.43), residues: 147
  loop : -0.26 (0.26), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 155 
 TYR   0.012   0.001   TYR A 403 
 PHE   0.012   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        0.00248 (10657)
  covalent geometry    : angle       0.46958 (14537)
  hydrogen bonds       : bond        0.03667 (  441)
  hydrogen bonds       : angle       4.14443 ( 1219)
  metal coordination   : bond        0.02128 (   12)
  metal coordination   : angle       3.57516 (    8)

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

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

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 89
  time to evaluate  : 0.585 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  147 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8411 (mppt)
REVERT: B   33 ARG cc_start: 0.8121 (mtp180) cc_final: 0.7842 (mtp180)
REVERT: B  127 ASP cc_start: 0.8003 (m-30) cc_final: 0.7747 (m-30)
REVERT: B  204 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7929 (pm20)
REVERT: B  216 LYS cc_start: 0.8446 (mttt) cc_final: 0.8192 (mmtt)
  outliers start: 25
  outliers final: 17
  residues processed: 109
  average time/residue: 0.3137
  time to fit residues: 45.7003
Evaluate side-chains
  109 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 90
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 CYS
Chi-restraints excluded: chain A residue  147 LYS
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain A residue  269 SER
Chi-restraints excluded: chain B residue  204 GLU
Chi-restraints excluded: chain B residue  211 ASN
Chi-restraints excluded: chain B residue  289 ASP
Chi-restraints excluded: chain B residue  302 ARG
Chi-restraints excluded: chain B residue  475 ARG
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  503 THR
Chi-restraints excluded: chain C residue    6 LYS
Chi-restraints excluded: chain C residue   16 ILE
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue  115 GLU
Chi-restraints excluded: chain C residue  266 HIS
Chi-restraints excluded: chain C residue  269 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 19 optimal weight:    0.8980
   chunk 92 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9980
   chunk 90 optimal weight:    6.9990
   chunk 57 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 0 optimal weight:    9.9990
   chunk 30 optimal weight:    0.9990
   chunk 122 optimal weight:    8.9990
   chunk 105 optimal weight:    3.9990
   chunk 94 optimal weight:    1.9990
   overall best weight:    1.3786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.147828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.102517 restraints weight = 41468.364|
|-----------------------------------------------------------------------------|
r_work (start): 0.3159 rms_B_bonded: 2.39
r_work: 0.3030 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2914 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2917
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2917 r_free = 0.2917    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2917 r_free = 0.2917    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2917
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8502
moved from start:          0.1264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064  10669  Z= 0.161
  Angle     :  0.503   8.757  14545  Z= 0.257
  Chirality :  0.038   0.136   1635
  Planarity :  0.004   0.053   1766
  Dihedral  : 12.879 166.437   1801
  Min Nonbonded Distance : 1.725

Molprobity Statistics.
  All-atom Clashscore : 2.98
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.29 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 22.04 %
    Favored  : 75.54 %
  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:  0.88 (0.24), residues: 1234
  helix:  1.85 (0.24), residues: 478
  sheet:  0.28 (0.42), residues: 147
  loop : -0.33 (0.25), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  73 
 TYR   0.014   0.001   TYR A 403 
 PHE   0.015   0.001   PHE C  44 
 TRP   0.007   0.001   TRP A 346 
 HIS   0.004   0.001   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 (10657)
  covalent geometry    : angle       0.49516 (14537)
  hydrogen bonds       : bond        0.04132 (  441)
  hydrogen bonds       : angle       4.23887 ( 1219)
  metal coordination   : bond        0.02203 (   12)
  metal coordination   : angle       3.70776 (    8)

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

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

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 88
  time to evaluate  : 0.548 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  147 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8436 (mppt)
REVERT: B  121 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8596 (mp)
REVERT: B  127 ASP cc_start: 0.7968 (m-30) cc_final: 0.7709 (m-30)
REVERT: B  204 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.8017 (pm20)
REVERT: B  216 LYS cc_start: 0.8582 (mttt) cc_final: 0.8313 (mmtt)
REVERT: B  222 ASP cc_start: 0.8559 (OUTLIER) cc_final: 0.8121 (t70)
  outliers start: 26
  outliers final: 19
  residues processed: 108
  average time/residue: 0.2751
  time to fit residues: 39.6457
Evaluate side-chains
  107 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 84
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 CYS
Chi-restraints excluded: chain A residue  147 LYS
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain A residue  269 SER
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  204 GLU
Chi-restraints excluded: chain B residue  211 ASN
Chi-restraints excluded: chain B residue  222 ASP
Chi-restraints excluded: chain B residue  289 ASP
Chi-restraints excluded: chain B residue  302 ARG
Chi-restraints excluded: chain B residue  475 ARG
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  496 SER
Chi-restraints excluded: chain B residue  503 THR
Chi-restraints excluded: chain C residue    6 LYS
Chi-restraints excluded: chain C residue   16 ILE
Chi-restraints excluded: chain C residue   55 ASP
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue  115 GLU
Chi-restraints excluded: chain C residue  266 HIS
Chi-restraints excluded: chain C residue  269 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 88 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 114 optimal weight:    8.9990
   chunk 107 optimal weight:    0.1980
   chunk 33 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 28 optimal weight:    0.1980
   chunk 90 optimal weight:    5.9990
   chunk 36 optimal weight:    0.6980
   overall best weight:    0.6182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.149330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.104043 restraints weight = 41251.470|
|-----------------------------------------------------------------------------|
r_work (start): 0.3188 rms_B_bonded: 2.31
r_work: 0.3064 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2950 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.2950
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2954
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2954 r_free = 0.2954    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2954 r_free = 0.2954    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2954
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8470
moved from start:          0.1339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.070  10669  Z= 0.100
  Angle     :  0.474   9.121  14545  Z= 0.240
  Chirality :  0.037   0.139   1635
  Planarity :  0.004   0.051   1766
  Dihedral  : 12.727 166.287   1801
  Min Nonbonded Distance : 1.766

Molprobity Statistics.
  All-atom Clashscore : 2.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 22.41 %
    Favored  : 75.54 %
  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:  1.06 (0.25), residues: 1234
  helix:  2.05 (0.24), residues: 478
  sheet:  0.34 (0.43), residues: 147
  loop : -0.26 (0.26), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 155 
 TYR   0.011   0.001   TYR A 403 
 PHE   0.012   0.001   PHE C 243 
 TRP   0.005   0.001   TRP A 346 
 HIS   0.003   0.001   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 (10657)
  covalent geometry    : angle       0.46649 (14537)
  hydrogen bonds       : bond        0.03550 (  441)
  hydrogen bonds       : angle       4.06836 ( 1219)
  metal coordination   : bond        0.02175 (   12)
  metal coordination   : angle       3.67563 (    8)

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

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

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 92
  time to evaluate  : 0.720 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  147 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8437 (mppt)
REVERT: B   33 ARG cc_start: 0.8137 (mtp180) cc_final: 0.7888 (mtp180)
REVERT: B  127 ASP cc_start: 0.8057 (m-30) cc_final: 0.7831 (m-30)
REVERT: B  204 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.8005 (pm20)
REVERT: B  216 LYS cc_start: 0.8418 (mttt) cc_final: 0.8159 (mmtt)
REVERT: B  222 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.8075 (t70)
  outliers start: 22
  outliers final: 18
  residues processed: 112
  average time/residue: 0.2885
  time to fit residues: 43.4777
Evaluate side-chains
  109 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 88
  time to evaluate  : 0.564 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 CYS
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue  147 LYS
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  269 SER
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   75 CYS
Chi-restraints excluded: chain B residue  204 GLU
Chi-restraints excluded: chain B residue  211 ASN
Chi-restraints excluded: chain B residue  222 ASP
Chi-restraints excluded: chain B residue  289 ASP
Chi-restraints excluded: chain B residue  302 ARG
Chi-restraints excluded: chain B residue  475 ARG
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  484 SER
Chi-restraints excluded: chain B residue  496 SER
Chi-restraints excluded: chain B residue  503 THR
Chi-restraints excluded: chain C residue    6 LYS
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue  269 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 104 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9980
   chunk 100 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 118 optimal weight:    4.9990
   chunk 90 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9990
   chunk 121 optimal weight:    9.9990
   chunk 94 optimal weight:    4.9990
   chunk 58 optimal weight:    1.9990
   overall best weight:    1.1986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.147946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.101679 restraints weight = 41461.735|
|-----------------------------------------------------------------------------|
r_work (start): 0.3153 rms_B_bonded: 2.12
r_work: 0.3044 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2926 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2926
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2932
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2932 r_free = 0.2932    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2932 r_free = 0.2932    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2932
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8491
moved from start:          0.1433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068  10669  Z= 0.146
  Angle     :  0.497   9.176  14545  Z= 0.254
  Chirality :  0.037   0.138   1635
  Planarity :  0.004   0.052   1766
  Dihedral  : 12.808 167.363   1801
  Min Nonbonded Distance : 1.741

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 22.04 %
    Favored  : 75.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.92 (0.24), residues: 1234
  helix:  1.91 (0.24), residues: 478
  sheet:  0.20 (0.42), residues: 147
  loop : -0.29 (0.26), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 217 
 TYR   0.013   0.001   TYR A 403 
 PHE   0.016   0.001   PHE C 243 
 TRP   0.006   0.001   TRP A 346 
 HIS   0.003   0.001   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (10657)
  covalent geometry    : angle       0.48874 (14537)
  hydrogen bonds       : bond        0.03947 (  441)
  hydrogen bonds       : angle       4.16316 ( 1219)
  metal coordination   : bond        0.02250 (   12)
  metal coordination   : angle       3.82559 (    8)

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

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

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 88
  time to evaluate  : 0.539 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  147 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8483 (mppt)
REVERT: B  127 ASP cc_start: 0.7984 (m-30) cc_final: 0.7759 (m-30)
REVERT: B  204 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.8023 (pm20)
REVERT: B  216 LYS cc_start: 0.8522 (mttt) cc_final: 0.8256 (mmtt)
REVERT: B  222 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.8113 (t70)
REVERT: B  475 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7480 (tmm-80)
REVERT: C  185 MET cc_start: 0.4374 (mtm) cc_final: 0.4169 (mtm)
  outliers start: 27
  outliers final: 20
  residues processed: 112
  average time/residue: 0.2528
  time to fit residues: 38.5440
Evaluate side-chains
  113 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 89
  time to evaluate  : 0.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 CYS
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue  147 LYS
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain A residue  269 SER
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   75 CYS
Chi-restraints excluded: chain B residue  204 GLU
Chi-restraints excluded: chain B residue  211 ASN
Chi-restraints excluded: chain B residue  222 ASP
Chi-restraints excluded: chain B residue  289 ASP
Chi-restraints excluded: chain B residue  302 ARG
Chi-restraints excluded: chain B residue  475 ARG
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  484 SER
Chi-restraints excluded: chain B residue  496 SER
Chi-restraints excluded: chain B residue  503 THR
Chi-restraints excluded: chain C residue    6 LYS
Chi-restraints excluded: chain C residue   55 ASP
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue  115 GLU
Chi-restraints excluded: chain C residue  269 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 114 optimal weight:    0.0970
   chunk 94 optimal weight:    4.9990
   chunk 63 optimal weight:    0.8980
   chunk 106 optimal weight:    5.9990
   chunk 60 optimal weight:    0.6980
   chunk 124 optimal weight:    8.9990
   chunk 111 optimal weight:    7.9990
   chunk 104 optimal weight:    3.9990
   chunk 103 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.9382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.148497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.101959 restraints weight = 41090.489|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 2.16
r_work: 0.3055 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2939 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2941
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2941 r_free = 0.2941    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2941 r_free = 0.2941    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2941
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8478
moved from start:          0.1497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068  10669  Z= 0.121
  Angle     :  0.484   8.902  14545  Z= 0.247
  Chirality :  0.037   0.139   1635
  Planarity :  0.004   0.051   1766
  Dihedral  : 12.783 169.744   1801
  Min Nonbonded Distance : 1.764

Molprobity Statistics.
  All-atom Clashscore : 3.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 21.76 %
    Favored  : 75.82 %
  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:  0.97 (0.24), residues: 1234
  helix:  1.97 (0.24), residues: 478
  sheet:  0.17 (0.42), residues: 148
  loop : -0.28 (0.26), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 217 
 TYR   0.012   0.001   TYR A 403 
 PHE   0.017   0.001   PHE C 243 
 TRP   0.006   0.001   TRP A 346 
 HIS   0.003   0.001   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 (10657)
  covalent geometry    : angle       0.47685 (14537)
  hydrogen bonds       : bond        0.03723 (  441)
  hydrogen bonds       : angle       4.09327 ( 1219)
  metal coordination   : bond        0.02153 (   12)
  metal coordination   : angle       3.64029 (    8)

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

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

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 90
  time to evaluate  : 0.541 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  147 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8463 (mppt)
REVERT: B  127 ASP cc_start: 0.8015 (m-30) cc_final: 0.7785 (m-30)
REVERT: B  204 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7990 (pm20)
REVERT: B  216 LYS cc_start: 0.8470 (mttt) cc_final: 0.8201 (mmtt)
REVERT: B  222 ASP cc_start: 0.8538 (OUTLIER) cc_final: 0.8092 (t70)
REVERT: B  475 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7500 (tmm-80)
  outliers start: 26
  outliers final: 21
  residues processed: 112
  average time/residue: 0.2478
  time to fit residues: 37.3252
Evaluate side-chains
  115 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 90
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 CYS
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue  147 LYS
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain A residue  269 SER
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   75 CYS
Chi-restraints excluded: chain B residue  204 GLU
Chi-restraints excluded: chain B residue  211 ASN
Chi-restraints excluded: chain B residue  222 ASP
Chi-restraints excluded: chain B residue  289 ASP
Chi-restraints excluded: chain B residue  302 ARG
Chi-restraints excluded: chain B residue  475 ARG
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  484 SER
Chi-restraints excluded: chain B residue  496 SER
Chi-restraints excluded: chain B residue  503 THR
Chi-restraints excluded: chain C residue    6 LYS
Chi-restraints excluded: chain C residue   55 ASP
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue  115 GLU
Chi-restraints excluded: chain C residue  269 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 96 optimal weight:    0.7980
   chunk 106 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 46 optimal weight:    0.3980
   chunk 29 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9980
   chunk 64 optimal weight:    0.6980
   chunk 28 optimal weight:    0.5980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.149121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.102696 restraints weight = 41232.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 2.16
r_work: 0.3065 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2955 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2959
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2959 r_free = 0.2959    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2959 r_free = 0.2959    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2959
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
moved from start:          0.1561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.072  10669  Z= 0.104
  Angle     :  0.478   9.004  14545  Z= 0.242
  Chirality :  0.037   0.139   1635
  Planarity :  0.004   0.051   1766
  Dihedral  : 12.707 171.468   1801
  Min Nonbonded Distance : 1.783

Molprobity Statistics.
  All-atom Clashscore : 2.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 21.85 %
    Favored  : 76.00 %
  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:  1.05 (0.25), residues: 1234
  helix:  2.05 (0.24), residues: 478
  sheet:  0.24 (0.43), residues: 148
  loop : -0.25 (0.26), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 217 
 TYR   0.011   0.001   TYR A 403 
 PHE   0.015   0.001   PHE C 243 
 TRP   0.006   0.001   TRP A 346 
 HIS   0.003   0.001   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 (10657)
  covalent geometry    : angle       0.47041 (14537)
  hydrogen bonds       : bond        0.03518 (  441)
  hydrogen bonds       : angle       4.03946 ( 1219)
  metal coordination   : bond        0.02258 (   12)
  metal coordination   : angle       3.58790 (    8)

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

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

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2468 Ramachandran restraints generated.
    1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 91
  time to evaluate  : 0.436 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  147 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8445 (mppt)
REVERT: B   33 ARG cc_start: 0.8154 (mtp180) cc_final: 0.7922 (mtp180)
REVERT: B  127 ASP cc_start: 0.7967 (m-30) cc_final: 0.7748 (m-30)
REVERT: B  204 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7994 (pm20)
REVERT: B  216 LYS cc_start: 0.8428 (mttt) cc_final: 0.8181 (mmtt)
REVERT: B  222 ASP cc_start: 0.8512 (OUTLIER) cc_final: 0.8095 (t70)
REVERT: B  475 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7540 (tmm-80)
  outliers start: 23
  outliers final: 18
  residues processed: 110
  average time/residue: 0.2739
  time to fit residues: 40.5941
Evaluate side-chains
  110 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 88
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 CYS
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue  147 LYS
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain A residue  269 SER
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   75 CYS
Chi-restraints excluded: chain B residue  204 GLU
Chi-restraints excluded: chain B residue  211 ASN
Chi-restraints excluded: chain B residue  222 ASP
Chi-restraints excluded: chain B residue  289 ASP
Chi-restraints excluded: chain B residue  302 ARG
Chi-restraints excluded: chain B residue  475 ARG
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  496 SER
Chi-restraints excluded: chain C residue    6 LYS
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue  115 GLU
Chi-restraints excluded: chain C residue  269 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 90 optimal weight:    5.9990
   chunk 89 optimal weight:    2.9990
   chunk 6 optimal weight:    0.2980
   chunk 2 optimal weight:   10.0000
   chunk 94 optimal weight:    5.9990
   chunk 108 optimal weight:    0.0270
   chunk 61 optimal weight:    2.9990
   chunk 74 optimal weight:    0.6980
   chunk 54 optimal weight:    0.3980
   chunk 104 optimal weight:    4.9990
   overall best weight:    0.8840

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.148467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.102130 restraints weight = 41360.023|
|-----------------------------------------------------------------------------|
r_work (start): 0.3164 rms_B_bonded: 2.15
r_work: 0.3056 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2941 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2942
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2942 r_free = 0.2942    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2942 r_free = 0.2942    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2942
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8478
moved from start:          0.1603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070  10669  Z= 0.119
  Angle     :  0.485   8.876  14545  Z= 0.247
  Chirality :  0.037   0.140   1635
  Planarity :  0.004   0.051   1766
  Dihedral  : 12.705 173.635   1800
  Min Nonbonded Distance : 1.769

Molprobity Statistics.
  All-atom Clashscore : 2.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 22.04 %
    Favored  : 75.82 %
  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:  1.01 (0.25), residues: 1234
  helix:  1.99 (0.24), residues: 478
  sheet:  0.18 (0.43), residues: 148
  loop : -0.23 (0.26), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 217 
 TYR   0.012   0.001   TYR A 403 
 PHE   0.015   0.001   PHE C 243 
 TRP   0.006   0.001   TRP A 346 
 HIS   0.003   0.001   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 (10657)
  covalent geometry    : angle       0.47804 (14537)
  hydrogen bonds       : bond        0.03660 (  441)
  hydrogen bonds       : angle       4.05242 ( 1219)
  metal coordination   : bond        0.02243 (   12)
  metal coordination   : angle       3.57412 (    8)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6408.08 seconds
wall clock time: 109 minutes 10.77 seconds (6550.77 seconds total)