Starting phenix.real_space_refine
on Wed May 21 02:04:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pt6_17868/05_2025/8pt6_17868_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pt6_17868/05_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pt6_17868/05_2025/8pt6_17868.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pt6_17868/05_2025/8pt6_17868.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pt6_17868/05_2025/8pt6_17868_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pt6_17868/05_2025/8pt6_17868_trim.cif"
  }
  resolution = 3.03
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 12.95, per 1000 atoms: 0.63
  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: 5.34
  Conformation dependent library (CDL) restraints added in 2.2 seconds
  
  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: 9.97
  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: 7.54

  Time building geometry restraints manager: 6.49 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:             1.300
  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:             0.360
  Extract box with map and model:          0.810
  Check model and map are aligned:         0.140
  Set scattering table:                    0.200
  Process input model:                     65.140
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   71.010
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.06 (0.25), 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
 TRP   0.005   0.001   TRP C 183 
 HIS   0.002   0.001   HIS A 371 
 PHE   0.010   0.001   PHE C  44 
 TYR   0.009   0.001   TYR A 403 
 ARG   0.005   0.000   ARG B 475 

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

*********************** 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  : 1.597 
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: 0.5856
  time to fit residues: 91.9240
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  : 1.538 
-------------------------------------------------------------------------------
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 105 optimal weight:    2.9990
   chunk 94 optimal weight:    4.9990
   chunk 52 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9990
   chunk 72 optimal weight:    2.9990
   chunk 113 optimal weight:   10.0000
   overall best weight:    1.5990

-------------------------------------------------------------------------------
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 = 0.3805 r_free = 0.3805 target = 0.148064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.102597 restraints weight = 41852.242|
|-----------------------------------------------------------------------------|
r_work (start): 0.3164 rms_B_bonded: 2.34
r_work: 0.3044 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2934 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.2934
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2933
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2933 r_free = 0.2933    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2933 r_free = 0.2933    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2933
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8499
moved from start:          0.0716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  10669  Z= 0.180
  Angle     :  0.536   8.725  14545  Z= 0.274
  Chirality :  0.039   0.156   1635
  Planarity :  0.004   0.055   1766
  Dihedral  : 13.654 177.919   1829
  Min Nonbonded Distance : 1.714

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.13 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 23.16 %
    Favored  : 73.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.24), residues: 1234
  helix:  1.80 (0.24), residues: 478
  sheet:  0.42 (0.42), residues: 144
  loop : -0.30 (0.26), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 346 
 HIS   0.006   0.001   HIS A 367 
 PHE   0.015   0.001   PHE C  44 
 TYR   0.015   0.001   TYR A 403 
 ARG   0.004   0.000   ARG B  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04632 (  441)
  hydrogen bonds       : angle       4.60557 ( 1219)
  metal coordination   : bond        0.02167 (   12)
  metal coordination   : angle       3.91134 (    8)
  covalent geometry    : bond        0.00408 (10657)
  covalent geometry    : angle       0.52865 (14537)

*********************** 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
  115 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 84
  time to evaluate  : 1.732 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  121 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8560 (mp)
REVERT: B  222 ASP cc_start: 0.8526 (OUTLIER) cc_final: 0.8147 (t70)
  outliers start: 31
  outliers final: 19
  residues processed: 111
  average time/residue: 0.6123
  time to fit residues: 92.5196
Evaluate side-chains
  106 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 85
  time to evaluate  : 1.642 
-------------------------------------------------------------------------------
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  187 THR
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 8 optimal weight:   10.0000
   chunk 52 optimal weight:    0.7980
   chunk 58 optimal weight:    0.8980
   chunk 114 optimal weight:    7.9990
   chunk 67 optimal weight:    1.9990
   chunk 68 optimal weight:    0.5980
   chunk 49 optimal weight:    0.7980
   chunk 109 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 88 optimal weight:    1.9990
   chunk 118 optimal weight:    0.9980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3826 r_free = 0.3826 target = 0.149670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.103941 restraints weight = 41453.738|
|-----------------------------------------------------------------------------|
r_work (start): 0.3188 rms_B_bonded: 2.35
r_work: 0.3070 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2957 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2960
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2960 r_free = 0.2960    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2960 r_free = 0.2960    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2960
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8476
moved from start:          0.0873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069  10669  Z= 0.113
  Angle     :  0.483   9.096  14545  Z= 0.245
  Chirality :  0.037   0.138   1635
  Planarity :  0.004   0.052   1766
  Dihedral  : 13.178 170.803   1811
  Min Nonbonded Distance : 1.742

Molprobity Statistics.
  All-atom Clashscore : 2.93
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.57 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 23.44 %
    Favored  : 74.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.24), residues: 1234
  helix:  1.95 (0.24), residues: 478
  sheet:  0.50 (0.43), residues: 144
  loop : -0.29 (0.26), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 346 
 HIS   0.005   0.001   HIS A 367 
 PHE   0.011   0.001   PHE C  44 
 TYR   0.011   0.001   TYR A 403 
 ARG   0.005   0.000   ARG B 155 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03885 (  441)
  hydrogen bonds       : angle       4.30240 ( 1219)
  metal coordination   : bond        0.02142 (   12)
  metal coordination   : angle       3.64350 (    8)
  covalent geometry    : bond        0.00254 (10657)
  covalent geometry    : angle       0.47560 (14537)

*********************** 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
  110 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 89
  time to evaluate  : 1.663 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  147 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8412 (mppt)
REVERT: B   33 ARG cc_start: 0.8103 (mtp180) cc_final: 0.7745 (mtp180)
REVERT: B  219 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.7861 (mt-10)
  outliers start: 21
  outliers final: 13
  residues processed: 106
  average time/residue: 0.6754
  time to fit residues: 94.6061
Evaluate side-chains
  101 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 1.597 
-------------------------------------------------------------------------------
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 B residue   75 CYS
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  115 GLU
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 124 optimal weight:    8.9990
   chunk 48 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   chunk 107 optimal weight:    0.6980
   chunk 109 optimal weight:    2.9990
   chunk 5 optimal weight:    9.9990
   chunk 40 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 104 optimal weight:    3.9990
   overall best weight:    1.9388

-------------------------------------------------------------------------------
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 = 0.3773 r_free = 0.3773 target = 0.146009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.101250 restraints weight = 41466.300|
|-----------------------------------------------------------------------------|
r_work (start): 0.3142 rms_B_bonded: 2.14
r_work: 0.3022 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2909 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.2909
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2910
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2910 r_free = 0.2910    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2910 r_free = 0.2910    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2910
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8507
moved from start:          0.1210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059  10669  Z= 0.210
  Angle     :  0.542   8.666  14545  Z= 0.280
  Chirality :  0.039   0.160   1635
  Planarity :  0.004   0.055   1766
  Dihedral  : 13.378 168.517   1805
  Min Nonbonded Distance : 1.702

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.62 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 22.13 %
    Favored  : 74.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.24), residues: 1234
  helix:  1.58 (0.24), residues: 478
  sheet:  0.30 (0.42), residues: 142
  loop : -0.47 (0.25), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 346 
 HIS   0.005   0.001   HIS A 367 
 PHE   0.017   0.001   PHE C  44 
 TYR   0.015   0.001   TYR A 403 
 ARG   0.007   0.000   ARG C 217 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04672 (  441)
  hydrogen bonds       : angle       4.48101 ( 1219)
  metal coordination   : bond        0.02262 (   12)
  metal coordination   : angle       3.93018 (    8)
  covalent geometry    : bond        0.00480 (10657)
  covalent geometry    : angle       0.53434 (14537)

*********************** 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
  119 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 88
  time to evaluate  : 1.535 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  147 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8440 (mppt)
REVERT: B  121 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8616 (mp)
REVERT: B  222 ASP cc_start: 0.8565 (OUTLIER) cc_final: 0.8114 (t70)
REVERT: B  264 MET cc_start: 0.8938 (ptt) cc_final: 0.8695 (ptt)
REVERT: C  185 MET cc_start: 0.4632 (mtm) cc_final: 0.4399 (mtm)
  outliers start: 31
  outliers final: 23
  residues processed: 113
  average time/residue: 0.6279
  time to fit residues: 95.3846
Evaluate side-chains
  109 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 83
  time to evaluate  : 1.551 
-------------------------------------------------------------------------------
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 B residue   75 CYS
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  182 VAL
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  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   16 ILE
Chi-restraints excluded: chain C residue   17 THR
Chi-restraints excluded: chain C residue   55 ASP
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue  217 ARG
Chi-restraints excluded: chain C residue  238 VAL
Chi-restraints excluded: chain C residue  266 HIS
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 100 optimal weight:    0.6980
   chunk 81 optimal weight:    2.9990
   chunk 105 optimal weight:    2.9990
   chunk 12 optimal weight:    0.4980
   chunk 88 optimal weight:    3.9990
   chunk 98 optimal weight:   10.0000
   chunk 116 optimal weight:    3.9990
   chunk 57 optimal weight:    0.3980
   chunk 118 optimal weight:    0.0980
   chunk 53 optimal weight:    0.3980
   chunk 113 optimal weight:    6.9990
   overall best weight:    0.4180

-------------------------------------------------------------------------------
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 = 0.149477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.104455 restraints weight = 41391.658|
|-----------------------------------------------------------------------------|
r_work (start): 0.3191 rms_B_bonded: 2.31
r_work: 0.3068 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2955 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.2955
-------------------------------------------------------------------------------
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 = 0.35   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 = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2957
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8462
moved from start:          0.1224

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= 0.093
  Angle     :  0.478   9.050  14545  Z= 0.242
  Chirality :  0.037   0.140   1635
  Planarity :  0.004   0.051   1766
  Dihedral  : 13.047 166.285   1805
  Min Nonbonded Distance : 1.771

Molprobity Statistics.
  All-atom Clashscore : 3.03
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.24 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 22.32 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.24), residues: 1234
  helix:  1.97 (0.24), residues: 478
  sheet:  0.22 (0.43), residues: 147
  loop : -0.27 (0.26), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 346 
 HIS   0.004   0.001   HIS A 367 
 PHE   0.010   0.001   PHE C  44 
 TYR   0.010   0.001   TYR A 403 
 ARG   0.005   0.000   ARG C 217 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03536 (  441)
  hydrogen bonds       : angle       4.14488 ( 1219)
  metal coordination   : bond        0.02123 (   12)
  metal coordination   : angle       3.63821 (    8)
  covalent geometry    : bond        0.00208 (10657)
  covalent geometry    : angle       0.47003 (14537)

*********************** 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
  123 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 93
  time to evaluate  : 1.639 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  147 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8417 (mppt)
REVERT: B   33 ARG cc_start: 0.8145 (mtp180) cc_final: 0.7793 (mtp180)
REVERT: B  127 ASP cc_start: 0.7994 (m-30) cc_final: 0.7759 (m-30)
REVERT: B  204 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7933 (pm20)
REVERT: B  216 LYS cc_start: 0.8418 (mttt) cc_final: 0.8037 (mmtt)
REVERT: B  219 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.7944 (mt-10)
REVERT: C  217 ARG cc_start: 0.5788 (OUTLIER) cc_final: 0.5401 (ttt180)
  outliers start: 30
  outliers final: 20
  residues processed: 116
  average time/residue: 0.6009
  time to fit residues: 94.0833
Evaluate side-chains
  112 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 88
  time to evaluate  : 1.607 
-------------------------------------------------------------------------------
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 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  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    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  217 ARG
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 7 optimal weight:    5.9990
   chunk 76 optimal weight:    0.7980
   chunk 98 optimal weight:    1.9990
   chunk 115 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 91 optimal weight:    4.9990
   chunk 66 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   chunk 65 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   overall best weight:    1.2384

-------------------------------------------------------------------------------
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 = 0.147764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.102537 restraints weight = 41382.542|
|-----------------------------------------------------------------------------|
r_work (start): 0.3160 rms_B_bonded: 2.34
r_work: 0.3034 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2919 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.2919
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2922
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2922 r_free = 0.2922    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 = 0.2922 r_free = 0.2922    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2922
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8499
moved from start:          0.1332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064  10669  Z= 0.148
  Angle     :  0.497   8.794  14545  Z= 0.253
  Chirality :  0.037   0.137   1635
  Planarity :  0.004   0.053   1766
  Dihedral  : 13.098 166.374   1805
  Min Nonbonded Distance : 1.734

Molprobity Statistics.
  All-atom Clashscore : 3.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 22.50 %
    Favored  : 75.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.24), residues: 1234
  helix:  1.88 (0.24), residues: 478
  sheet:  0.13 (0.42), residues: 147
  loop : -0.33 (0.26), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 346 
 HIS   0.003   0.001   HIS A 367 
 PHE   0.014   0.001   PHE C  44 
 TYR   0.013   0.001   TYR A 403 
 ARG   0.006   0.000   ARG C 217 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04005 (  441)
  hydrogen bonds       : angle       4.21196 ( 1219)
  metal coordination   : bond        0.02128 (   12)
  metal coordination   : angle       3.67395 (    8)
  covalent geometry    : bond        0.00339 (10657)
  covalent geometry    : angle       0.48911 (14537)

*********************** 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
  115 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 89
  time to evaluate  : 1.495 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  147 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8458 (mppt)
REVERT: B   33 ARG cc_start: 0.8128 (mtp180) cc_final: 0.7790 (mtp180)
REVERT: B  127 ASP cc_start: 0.7965 (m-30) cc_final: 0.7730 (m-30)
REVERT: B  204 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7966 (pm20)
REVERT: B  475 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7498 (tmm-80)
REVERT: C  217 ARG cc_start: 0.5825 (OUTLIER) cc_final: 0.5451 (ttt180)
  outliers start: 26
  outliers final: 17
  residues processed: 111
  average time/residue: 0.6183
  time to fit residues: 92.7050
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  : 1.607 
-------------------------------------------------------------------------------
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 B residue   65 VAL
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  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   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  217 ARG
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 112 optimal weight:    8.9990
   chunk 0 optimal weight:    8.9990
   chunk 75 optimal weight:    2.9990
   chunk 103 optimal weight:    1.9990
   chunk 7 optimal weight:    5.9990
   chunk 33 optimal weight:    0.7980
   chunk 114 optimal weight:    0.8980
   chunk 78 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 90 optimal weight:    5.9990
   chunk 44 optimal weight:    2.9990
   overall best weight:    1.0982

-------------------------------------------------------------------------------
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 = 0.3797 r_free = 0.3797 target = 0.147864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.102515 restraints weight = 41364.438|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 2.37
r_work: 0.3037 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2922 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2925
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2925 r_free = 0.2925    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 = 0.2925 r_free = 0.2925    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2925
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.1454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067  10669  Z= 0.133
  Angle     :  0.491   9.052  14545  Z= 0.250
  Chirality :  0.037   0.138   1635
  Planarity :  0.004   0.052   1766
  Dihedral  : 12.861 166.471   1801
  Min Nonbonded Distance : 1.744

Molprobity Statistics.
  All-atom Clashscore : 2.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 22.32 %
    Favored  : 75.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.24), residues: 1234
  helix:  1.88 (0.24), residues: 478
  sheet:  0.12 (0.42), residues: 147
  loop : -0.33 (0.25), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 346 
 HIS   0.004   0.001   HIS A 367 
 PHE   0.015   0.001   PHE C 243 
 TYR   0.013   0.001   TYR A 403 
 ARG   0.006   0.000   ARG C 217 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03882 (  441)
  hydrogen bonds       : angle       4.16693 ( 1219)
  metal coordination   : bond        0.02144 (   12)
  metal coordination   : angle       3.77661 (    8)
  covalent geometry    : bond        0.00302 (10657)
  covalent geometry    : angle       0.48337 (14537)

*********************** 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: 25
    poor density    : 89
  time to evaluate  : 1.767 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  147 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8472 (mppt)
REVERT: B   33 ARG cc_start: 0.8119 (mtp180) cc_final: 0.7784 (mtp180)
REVERT: B  127 ASP cc_start: 0.8007 (m-30) cc_final: 0.7765 (m-30)
REVERT: B  204 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7969 (pm20)
REVERT: B  216 LYS cc_start: 0.8463 (mttt) cc_final: 0.8015 (mmtt)
REVERT: B  219 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.7850 (mt-10)
REVERT: B  222 ASP cc_start: 0.8553 (OUTLIER) cc_final: 0.8122 (t70)
REVERT: B  475 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7520 (tmm-80)
  outliers start: 25
  outliers final: 17
  residues processed: 110
  average time/residue: 0.6134
  time to fit residues: 91.5850
Evaluate side-chains
  111 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 89
  time to evaluate  : 1.465 
-------------------------------------------------------------------------------
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 B residue   65 VAL
Chi-restraints excluded: chain B residue  204 GLU
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  337 ASP
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    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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 89 optimal weight:    3.9990
   chunk 8 optimal weight:    7.9990
   chunk 70 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 85 optimal weight:    0.1980
   chunk 51 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 118 optimal weight:    7.9990
   overall best weight:    1.6388

-------------------------------------------------------------------------------
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 = 0.3775 r_free = 0.3775 target = 0.146153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.100704 restraints weight = 41566.508|
|-----------------------------------------------------------------------------|
r_work (start): 0.3133 rms_B_bonded: 2.46
r_work: 0.3007 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2890 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2890
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2890
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2890 r_free = 0.2890    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2890 r_free = 0.2890    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2890
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8523
moved from start:          0.1625

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= 0.186
  Angle     :  0.524   9.126  14545  Z= 0.270
  Chirality :  0.039   0.145   1635
  Planarity :  0.004   0.053   1766
  Dihedral  : 13.043 168.100   1801
  Min Nonbonded Distance : 1.714

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.46 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 22.22 %
    Favored  : 75.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.24), residues: 1234
  helix:  1.67 (0.24), residues: 478
  sheet: -0.02 (0.42), residues: 147
  loop : -0.42 (0.25), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 346 
 HIS   0.004   0.001   HIS A 367 
 PHE   0.016   0.001   PHE C  44 
 TYR   0.014   0.001   TYR A 403 
 ARG   0.006   0.000   ARG C 217 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04422 (  441)
  hydrogen bonds       : angle       4.32711 ( 1219)
  metal coordination   : bond        0.02319 (   12)
  metal coordination   : angle       4.07934 (    8)
  covalent geometry    : bond        0.00425 (10657)
  covalent geometry    : angle       0.51538 (14537)

*********************** 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
  111 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 85
  time to evaluate  : 1.623 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  147 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8514 (mppt)
REVERT: B   33 ARG cc_start: 0.8116 (mtp180) cc_final: 0.7755 (mtp180)
REVERT: B  204 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7921 (pm20)
REVERT: B  219 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.7804 (mt-10)
REVERT: B  222 ASP cc_start: 0.8575 (OUTLIER) cc_final: 0.8132 (t70)
REVERT: B  264 MET cc_start: 0.8946 (ptt) cc_final: 0.8674 (ptt)
REVERT: B  475 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7566 (tmm-80)
  outliers start: 26
  outliers final: 19
  residues processed: 107
  average time/residue: 0.6110
  time to fit residues: 88.9957
Evaluate side-chains
  108 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 84
  time to evaluate  : 1.611 
-------------------------------------------------------------------------------
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 B residue   65 VAL
Chi-restraints excluded: chain B residue  204 GLU
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  337 ASP
Chi-restraints excluded: chain B residue  475 ARG
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   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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9980
   chunk 109 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 8 optimal weight:    9.9990
   chunk 100 optimal weight:    1.9990
   chunk 96 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 117 optimal weight:    0.8980
   chunk 115 optimal weight:    0.4980
   chunk 53 optimal weight:    0.5980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3799 r_free = 0.3799 target = 0.148039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.102999 restraints weight = 41240.885|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 2.35
r_work: 0.3046 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2932 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.2932
-------------------------------------------------------------------------------
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 = 0.30   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: 0.8492
moved from start:          0.1615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072  10669  Z= 0.109
  Angle     :  0.484   9.375  14545  Z= 0.246
  Chirality :  0.037   0.140   1635
  Planarity :  0.004   0.052   1766
  Dihedral  : 12.888 169.902   1801
  Min Nonbonded Distance : 1.759

Molprobity Statistics.
  All-atom Clashscore : 3.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 22.78 %
    Favored  : 75.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.24), residues: 1234
  helix:  1.91 (0.24), residues: 478
  sheet:  0.08 (0.43), residues: 146
  loop : -0.35 (0.26), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 346 
 HIS   0.004   0.001   HIS A 367 
 PHE   0.015   0.001   PHE C 243 
 TYR   0.011   0.001   TYR A 403 
 ARG   0.005   0.000   ARG C 217 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03677 (  441)
  hydrogen bonds       : angle       4.11980 ( 1219)
  metal coordination   : bond        0.02223 (   12)
  metal coordination   : angle       3.75628 (    8)
  covalent geometry    : bond        0.00244 (10657)
  covalent geometry    : angle       0.47620 (14537)

*********************** 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
  107 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 86
  time to evaluate  : 1.504 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  147 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8476 (mppt)
REVERT: B   33 ARG cc_start: 0.8135 (mtp180) cc_final: 0.7804 (mtp180)
REVERT: B  127 ASP cc_start: 0.8019 (m-30) cc_final: 0.7764 (m-30)
REVERT: B  204 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7980 (pm20)
REVERT: B  216 LYS cc_start: 0.8441 (mttt) cc_final: 0.8000 (mmtt)
REVERT: B  219 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.7843 (mt-10)
REVERT: B  475 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7608 (tmm-80)
  outliers start: 21
  outliers final: 14
  residues processed: 103
  average time/residue: 0.6204
  time to fit residues: 86.0608
Evaluate side-chains
  102 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 84
  time to evaluate  : 1.665 
-------------------------------------------------------------------------------
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 B residue  204 GLU
Chi-restraints excluded: chain B residue  211 ASN
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  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 66 optimal weight:    0.0670
   chunk 62 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 106 optimal weight:    5.9990
   chunk 1 optimal weight:   10.0000
   chunk 55 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 113 optimal weight:   10.0000
   chunk 97 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.3524

-------------------------------------------------------------------------------
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 = 0.3783 r_free = 0.3783 target = 0.146759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.100911 restraints weight = 41217.374|
|-----------------------------------------------------------------------------|
r_work (start): 0.3140 rms_B_bonded: 2.11
r_work: 0.3029 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2918 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.2918
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2920
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2920 r_free = 0.2920    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 = 0.2920 r_free = 0.2920    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2920
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8493
moved from start:          0.1697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069  10669  Z= 0.156
  Angle     :  0.504   9.094  14545  Z= 0.258
  Chirality :  0.038   0.137   1635
  Planarity :  0.004   0.053   1766
  Dihedral  : 12.962 171.429   1801
  Min Nonbonded Distance : 1.742

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.05 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 22.78 %
    Favored  : 75.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.24), residues: 1234
  helix:  1.79 (0.24), residues: 478
  sheet: -0.03 (0.42), residues: 146
  loop : -0.40 (0.25), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 346 
 HIS   0.004   0.001   HIS A 367 
 PHE   0.015   0.001   PHE C 243 
 TYR   0.013   0.001   TYR A 403 
 ARG   0.005   0.000   ARG C 217 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04066 (  441)
  hydrogen bonds       : angle       4.22017 ( 1219)
  metal coordination   : bond        0.02299 (   12)
  metal coordination   : angle       3.91302 (    8)
  covalent geometry    : bond        0.00355 (10657)
  covalent geometry    : angle       0.49610 (14537)

********************** 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
  104 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 83
  time to evaluate  : 1.531 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  147 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8494 (mppt)
REVERT: B   33 ARG cc_start: 0.8120 (mtp180) cc_final: 0.7767 (mtp180)
REVERT: B  204 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7939 (pm20)
REVERT: B  216 LYS cc_start: 0.8542 (mttt) cc_final: 0.8084 (mmtt)
REVERT: B  219 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.7809 (mt-10)
REVERT: B  475 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7622 (tmm-80)
  outliers start: 21
  outliers final: 17
  residues processed: 101
  average time/residue: 0.6198
  time to fit residues: 84.1697
Evaluate side-chains
  104 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 83
  time to evaluate  : 1.522 
-------------------------------------------------------------------------------
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 B residue   65 VAL
Chi-restraints excluded: chain B residue  204 GLU
Chi-restraints excluded: chain B residue  211 ASN
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  337 ASP
Chi-restraints excluded: chain B residue  475 ARG
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 2 optimal weight:   10.0000
   chunk 43 optimal weight:    1.9990
   chunk 85 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 94 optimal weight:    0.9990
   chunk 116 optimal weight:    3.9990
   chunk 59 optimal weight:    3.9990
   chunk 0 optimal weight:    9.9990
   chunk 99 optimal weight:    1.9990
   chunk 119 optimal weight:   10.0000
   overall best weight:    1.7990

-------------------------------------------------------------------------------
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 = 0.3767 r_free = 0.3767 target = 0.145412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.100145 restraints weight = 41686.622|
|-----------------------------------------------------------------------------|
r_work (start): 0.3114 rms_B_bonded: 2.43
r_work: 0.2992 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2877 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2877
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2878
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2878 r_free = 0.2878    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2878 r_free = 0.2878    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2878
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8525
moved from start:          0.1830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065  10669  Z= 0.198
  Angle     :  0.534   8.419  14545  Z= 0.275
  Chirality :  0.039   0.144   1635
  Planarity :  0.004   0.053   1766
  Dihedral  : 13.190 174.087   1801
  Min Nonbonded Distance : 1.717

Molprobity Statistics.
  All-atom Clashscore : 3.23
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.62 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 22.88 %
    Favored  : 75.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.24), residues: 1234
  helix:  1.58 (0.24), residues: 478
  sheet: -0.11 (0.42), residues: 146
  loop : -0.49 (0.25), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 346 
 HIS   0.004   0.001   HIS A 367 
 PHE   0.017   0.001   PHE C  44 
 TYR   0.015   0.001   TYR A 403 
 ARG   0.005   0.000   ARG C 217 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04541 (  441)
  hydrogen bonds       : angle       4.36429 ( 1219)
  metal coordination   : bond        0.02369 (   12)
  metal coordination   : angle       4.06441 (    8)
  covalent geometry    : bond        0.00453 (10657)
  covalent geometry    : angle       0.52606 (14537)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 12715.19 seconds
wall clock time: 217 minutes 57.11 seconds (13077.11 seconds total)