Starting phenix.real_space_refine
on Wed Jun 18 04:58:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pt6_17868/06_2025/8pt6_17868_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pt6_17868/06_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_17868/06_2025/8pt6_17868.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pt6_17868/06_2025/8pt6_17868.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pt6_17868/06_2025/8pt6_17868_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pt6_17868/06_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-5710/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: 13.56, per 1000 atoms: 0.66
  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: 5.68
  Conformation dependent library (CDL) restraints added in 2.0 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: 10.17
  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: 8.18

  Time building geometry restraints manager: 6.78 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:             1.440
  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:          0.770
  Check model and map are aligned:         0.170
  Set scattering table:                    0.210
  Process input model:                     67.040
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.080
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   73.250
-------------------------------------------------------------------------------
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  : 1.470 
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: 0.5785
  time to fit residues: 90.7702
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  : 1.445 
-------------------------------------------------------------------------------
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 = 0.3807 r_free = 0.3807 target = 0.148159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.102358 restraints weight = 41887.716|
|-----------------------------------------------------------------------------|
r_work (start): 0.3165 rms_B_bonded: 2.32
r_work: 0.3046 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2937 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2936
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2936 r_free = 0.2936    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2936 r_free = 0.2936    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2936
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8497
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       3.91133 (    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  : 1.720 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  121 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8563 (mp)
REVERT: B  222 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.8156 (t70)
  outliers start: 31
  outliers final: 19
  residues processed: 111
  average time/residue: 0.6232
  time to fit residues: 94.7352
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  : 1.603 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 58 optimal weight:    0.5980
   chunk 114 optimal weight:    7.9990
   chunk 67 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   chunk 49 optimal weight:    1.9990
   chunk 109 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 88 optimal weight:    2.9990
   chunk 118 optimal weight:    0.9980
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 = 0.3818 r_free = 0.3818 target = 0.149052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.103518 restraints weight = 41468.002|
|-----------------------------------------------------------------------------|
r_work (start): 0.3180 rms_B_bonded: 2.42
r_work: 0.3059 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2949 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.2949
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2950
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2950 r_free = 0.2950    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2950 r_free = 0.2950    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2950
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.0906

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= 0.129
  Angle     :  0.491   9.042  14545  Z= 0.249
  Chirality :  0.037   0.136   1635
  Planarity :  0.004   0.053   1766
  Dihedral  : 13.233 170.226   1811
  Min Nonbonded Distance : 1.729

Molprobity Statistics.
  All-atom Clashscore : 3.03
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.89 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 23.06 %
    Favored  : 74.79 %
  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:  0.95 (0.24), residues: 1234
  helix:  1.89 (0.24), residues: 478
  sheet:  0.47 (0.43), residues: 144
  loop : -0.32 (0.26), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 346 
 HIS   0.005   0.001   HIS A 367 
 PHE   0.012   0.001   PHE C  44 
 TYR   0.012   0.001   TYR A 403 
 ARG   0.005   0.000   ARG B 155 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04057 (  441)
  hydrogen bonds       : angle       4.33794 ( 1219)
  metal coordination   : bond        0.02126 (   12)
  metal coordination   : angle       3.68470 (    8)
  covalent geometry    : bond        0.00292 (10657)
  covalent geometry    : angle       0.48339 (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: 23
    poor density    : 87
  time to evaluate  : 1.746 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  147 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8426 (mppt)
REVERT: B   33 ARG cc_start: 0.8121 (mtp180) cc_final: 0.7737 (mtp180)
REVERT: B  219 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.7921 (mt-10)
  outliers start: 23
  outliers final: 15
  residues processed: 107
  average time/residue: 0.6747
  time to fit residues: 95.3210
Evaluate side-chains
  101 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 84
  time to evaluate  : 1.694 
-------------------------------------------------------------------------------
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  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   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:    0.9990
   chunk 29 optimal weight:    3.9990
   chunk 107 optimal weight:    2.9990
   chunk 109 optimal weight:    3.9990
   chunk 5 optimal weight:    9.9990
   chunk 40 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 104 optimal weight:    2.9990
   overall best weight:    1.9788

-------------------------------------------------------------------------------
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 = 0.146094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.100564 restraints weight = 41620.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.3132 rms_B_bonded: 2.22
r_work: 0.3011 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2899 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2898
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2898 r_free = 0.2898    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2898 r_free = 0.2898    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2898
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8517
moved from start:          0.1258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  10669  Z= 0.215
  Angle     :  0.547   8.846  14545  Z= 0.282
  Chirality :  0.039   0.157   1635
  Planarity :  0.005   0.055   1766
  Dihedral  : 13.431 168.508   1806
  Min Nonbonded Distance : 1.699

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.70 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 21.85 %
    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:  0.56 (0.24), residues: 1234
  helix:  1.52 (0.24), residues: 478
  sheet:  0.25 (0.42), residues: 142
  loop : -0.50 (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   0.018   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        0.04727 (  441)
  hydrogen bonds       : angle       4.50057 ( 1219)
  metal coordination   : bond        0.02305 (   12)
  metal coordination   : angle       4.01486 (    8)
  covalent geometry    : bond        0.00492 (10657)
  covalent geometry    : angle       0.53918 (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
  121 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 88
  time to evaluate  : 1.501 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  147 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8442 (mppt)
REVERT: B  121 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8631 (mp)
REVERT: B  222 ASP cc_start: 0.8578 (OUTLIER) cc_final: 0.8129 (t70)
REVERT: B  264 MET cc_start: 0.8951 (ptt) cc_final: 0.8710 (ptt)
REVERT: C  185 MET cc_start: 0.4687 (mtm) cc_final: 0.4475 (mtm)
  outliers start: 33
  outliers final: 23
  residues processed: 114
  average time/residue: 0.6230
  time to fit residues: 96.6716
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  : 1.567 
-------------------------------------------------------------------------------
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  121 LEU
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  187 THR
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  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  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:    0.9980
   chunk 81 optimal weight:    2.9990
   chunk 105 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 88 optimal weight:    3.9990
   chunk 98 optimal weight:   10.0000
   chunk 116 optimal weight:    5.9990
   chunk 57 optimal weight:    0.4980
   chunk 118 optimal weight:    0.0670
   chunk 53 optimal weight:    0.9980
   chunk 113 optimal weight:    7.9990
   overall best weight:    0.6918

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.148493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.103587 restraints weight = 41246.855|
|-----------------------------------------------------------------------------|
r_work (start): 0.3175 rms_B_bonded: 2.34
r_work: 0.3049 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2935 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2936
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2936 r_free = 0.2936    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2936 r_free = 0.2936    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2936
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8479
moved from start:          0.1297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.068  10669  Z= 0.106
  Angle     :  0.484   9.101  14545  Z= 0.246
  Chirality :  0.037   0.139   1635
  Planarity :  0.004   0.052   1766
  Dihedral  : 13.146 166.387   1805
  Min Nonbonded Distance : 1.752

Molprobity Statistics.
  All-atom Clashscore : 3.13
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.32 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 22.32 %
    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:  1.87 (0.24), residues: 478
  sheet:  0.16 (0.42), residues: 147
  loop : -0.35 (0.25), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   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   0.004   0.000   ARG C 217 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03738 (  441)
  hydrogen bonds       : angle       4.20272 ( 1219)
  metal coordination   : bond        0.02084 (   12)
  metal coordination   : angle       3.73095 (    8)
  covalent geometry    : bond        0.00236 (10657)
  covalent geometry    : angle       0.47585 (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
  120 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 92
  time to evaluate  : 1.610 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  147 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8427 (mppt)
REVERT: B   33 ARG cc_start: 0.8139 (mtp180) cc_final: 0.7859 (mtp180)
REVERT: B  127 ASP cc_start: 0.7967 (m-30) cc_final: 0.7720 (m-30)
REVERT: B  204 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7945 (pm20)
REVERT: B  475 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.7434 (tmm-80)
  outliers start: 28
  outliers final: 17
  residues processed: 113
  average time/residue: 0.6256
  time to fit residues: 96.1721
Evaluate side-chains
  108 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 88
  time to evaluate  : 1.637 
-------------------------------------------------------------------------------
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  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  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   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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 7 optimal weight:    9.9990
   chunk 76 optimal weight:    0.9990
   chunk 98 optimal weight:    1.9990
   chunk 115 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 91 optimal weight:    4.9990
   chunk 66 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   overall best weight:    1.3788

-------------------------------------------------------------------------------
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 = 0.3784 r_free = 0.3784 target = 0.146896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.102083 restraints weight = 41205.913|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 2.34
r_work: 0.3023 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2908 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2908
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2908 r_free = 0.2908    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2908 r_free = 0.2908    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2908
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8507
moved from start:          0.1434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066  10669  Z= 0.163
  Angle     :  0.508   9.158  14545  Z= 0.260
  Chirality :  0.038   0.139   1635
  Planarity :  0.004   0.054   1766
  Dihedral  : 13.005 166.447   1802
  Min Nonbonded Distance : 1.724

Molprobity Statistics.
  All-atom Clashscore : 3.03
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.38 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 22.13 %
    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:  0.73 (0.24), residues: 1234
  helix:  1.74 (0.24), residues: 478
  sheet:  0.10 (0.42), residues: 147
  loop : -0.40 (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   0.015   0.001   PHE C  44 
 TYR   0.014   0.001   TYR A 403 
 ARG   0.004   0.000   ARG C 217 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04198 (  441)
  hydrogen bonds       : angle       4.28126 ( 1219)
  metal coordination   : bond        0.02251 (   12)
  metal coordination   : angle       3.94736 (    8)
  covalent geometry    : bond        0.00372 (10657)
  covalent geometry    : angle       0.49922 (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
  114 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 87
  time to evaluate  : 1.563 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  147 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8470 (mppt)
REVERT: B   33 ARG cc_start: 0.8106 (mtp180) cc_final: 0.7816 (mtp180)
REVERT: B  127 ASP cc_start: 0.7973 (m-30) cc_final: 0.7736 (m-30)
REVERT: B  204 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7929 (pm20)
REVERT: B  222 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.8132 (t70)
REVERT: B  475 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7524 (tmm-80)
  outliers start: 27
  outliers final: 21
  residues processed: 108
  average time/residue: 0.6256
  time to fit residues: 91.9471
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  : 1.576 
-------------------------------------------------------------------------------
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  248 SER
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  187 THR
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  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  266 HIS
Chi-restraints excluded: chain C residue  269 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 112 optimal weight:    8.9990
   chunk 0 optimal weight:    9.9990
   chunk 75 optimal weight:    2.9990
   chunk 103 optimal weight:    1.9990
   chunk 7 optimal weight:    9.9990
   chunk 33 optimal weight:    0.7980
   chunk 114 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 90 optimal weight:    5.9990
   chunk 44 optimal weight:    2.9990
   overall best weight:    1.9586

-------------------------------------------------------------------------------
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 = 0.3766 r_free = 0.3766 target = 0.145403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.100165 restraints weight = 41530.259|
|-----------------------------------------------------------------------------|
r_work (start): 0.3123 rms_B_bonded: 2.41
r_work: 0.2995 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2878 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2879
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2879 r_free = 0.2879    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 = 0.2879 r_free = 0.2879    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2879
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8538
moved from start:          0.1687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061  10669  Z= 0.213
  Angle     :  0.542   8.726  14545  Z= 0.280
  Chirality :  0.040   0.145   1635
  Planarity :  0.005   0.054   1766
  Dihedral  : 13.226 166.892   1801
  Min Nonbonded Distance : 1.697

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.86 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 21.85 %
    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:  0.46 (0.24), residues: 1234
  helix:  1.48 (0.24), residues: 478
  sheet: -0.06 (0.42), residues: 147
  loop : -0.51 (0.25), residues: 609

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   0.018   0.001   PHE C  44 
 TYR   0.015   0.001   TYR A 403 
 ARG   0.005   0.000   ARG B  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04716 (  441)
  hydrogen bonds       : angle       4.42593 ( 1219)
  metal coordination   : bond        0.02316 (   12)
  metal coordination   : angle       4.16350 (    8)
  covalent geometry    : bond        0.00486 (10657)
  covalent geometry    : angle       0.53331 (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
  115 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 82
  time to evaluate  : 1.610 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  147 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8536 (mppt)
REVERT: B  204 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7911 (pm20)
REVERT: B  219 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8134 (mt-10)
REVERT: B  222 ASP cc_start: 0.8582 (OUTLIER) cc_final: 0.8140 (t70)
REVERT: B  264 MET cc_start: 0.8946 (ptt) cc_final: 0.8651 (ptt)
  outliers start: 33
  outliers final: 22
  residues processed: 109
  average time/residue: 0.6208
  time to fit residues: 90.8080
Evaluate side-chains
  108 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 82
  time to evaluate  : 1.453 
-------------------------------------------------------------------------------
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  182 VAL
Chi-restraints excluded: chain B residue  187 THR
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  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  238 VAL
Chi-restraints excluded: chain C residue  266 HIS
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:    1.9990
   chunk 89 optimal weight:    3.9990
   chunk 8 optimal weight:    7.9990
   chunk 70 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 84 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9980
   chunk 85 optimal weight:    0.0970
   chunk 51 optimal weight:    0.7980
   chunk 68 optimal weight:    1.9990
   chunk 118 optimal weight:    6.9990
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 = 0.3786 r_free = 0.3786 target = 0.147072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.102277 restraints weight = 41385.024|
|-----------------------------------------------------------------------------|
r_work (start): 0.3158 rms_B_bonded: 2.28
r_work: 0.3034 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2917 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2917
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2919
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2919 r_free = 0.2919    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2919 r_free = 0.2919    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2919
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8497
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      :  0.003   0.070  10669  Z= 0.121
  Angle     :  0.494   9.247  14545  Z= 0.252
  Chirality :  0.037   0.136   1635
  Planarity :  0.004   0.052   1766
  Dihedral  : 12.979 166.597   1797
  Min Nonbonded Distance : 1.741

Molprobity Statistics.
  All-atom Clashscore : 2.98
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.73 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 22.60 %
    Favored  : 75.16 %
  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:  0.69 (0.24), residues: 1234
  helix:  1.75 (0.24), residues: 478
  sheet: -0.02 (0.42), residues: 147
  loop : -0.44 (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   0.013   0.001   PHE C 243 
 TYR   0.011   0.001   TYR A 403 
 ARG   0.004   0.000   ARG C 217 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03913 (  441)
  hydrogen bonds       : angle       4.22415 ( 1219)
  metal coordination   : bond        0.02196 (   12)
  metal coordination   : angle       3.96236 (    8)
  covalent geometry    : bond        0.00274 (10657)
  covalent geometry    : angle       0.48489 (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
  109 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 85
  time to evaluate  : 1.733 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  147 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8474 (mppt)
REVERT: A  317 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.7894 (ttm170)
REVERT: B   33 ARG cc_start: 0.8129 (mtp180) cc_final: 0.7856 (mtp180)
REVERT: B  204 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7952 (pm20)
REVERT: B  264 MET cc_start: 0.8903 (ptt) cc_final: 0.8648 (ptt)
  outliers start: 24
  outliers final: 20
  residues processed: 105
  average time/residue: 0.6404
  time to fit residues: 91.0786
Evaluate side-chains
  106 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 83
  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  248 SER
Chi-restraints excluded: chain A residue  317 ARG
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  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  269 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 57 optimal weight:    0.9980
   chunk 109 optimal weight:    0.9980
   chunk 34 optimal weight:    0.8980
   chunk 8 optimal weight:    5.9990
   chunk 100 optimal weight:    0.8980
   chunk 96 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 117 optimal weight:    3.9990
   chunk 115 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   overall best weight:    0.9380

-------------------------------------------------------------------------------
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 = 0.3791 r_free = 0.3791 target = 0.147342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.102217 restraints weight = 41202.300|
|-----------------------------------------------------------------------------|
r_work (start): 0.3156 rms_B_bonded: 2.34
r_work: 0.3033 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2919 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.2919
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2921
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2921 r_free = 0.2921    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 = 0.2921 r_free = 0.2921    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2921
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.1737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070  10669  Z= 0.124
  Angle     :  0.489   9.158  14545  Z= 0.250
  Chirality :  0.037   0.138   1635
  Planarity :  0.004   0.052   1766
  Dihedral  : 12.912 166.416   1797
  Min Nonbonded Distance : 1.751

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.81 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 22.97 %
    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:  0.74 (0.24), residues: 1234
  helix:  1.81 (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   0.006   0.001   TRP A 346 
 HIS   0.004   0.001   HIS A 367 
 PHE   0.015   0.001   PHE C 243 
 TYR   0.012   0.001   TYR A 403 
 ARG   0.004   0.000   ARG C 217 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03860 (  441)
  hydrogen bonds       : angle       4.18027 ( 1219)
  metal coordination   : bond        0.02237 (   12)
  metal coordination   : angle       3.86259 (    8)
  covalent geometry    : bond        0.00281 (10657)
  covalent geometry    : angle       0.48096 (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
  104 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 83
  time to evaluate  : 1.644 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  147 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8504 (mppt)
REVERT: B   33 ARG cc_start: 0.8132 (mtp180) cc_final: 0.7856 (mtp180)
REVERT: B  127 ASP cc_start: 0.7964 (m-30) cc_final: 0.7724 (m-30)
REVERT: B  204 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7958 (pm20)
REVERT: B  475 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7340 (tmm-80)
  outliers start: 21
  outliers final: 18
  residues processed: 101
  average time/residue: 0.6280
  time to fit residues: 86.3694
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  : 1.509 
-------------------------------------------------------------------------------
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  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  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  269 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 66 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 106 optimal weight:   10.0000
   chunk 1 optimal weight:    9.9990
   chunk 55 optimal weight:    0.8980
   chunk 29 optimal weight:    3.9990
   chunk 113 optimal weight:    8.9990
   chunk 97 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 0 optimal weight:    9.9990
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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 = 0.3779 r_free = 0.3779 target = 0.146482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.101796 restraints weight = 41265.548|
|-----------------------------------------------------------------------------|
r_work (start): 0.3144 rms_B_bonded: 2.32
r_work: 0.3019 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2905 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.2905
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2906
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2906 r_free = 0.2906    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2906 r_free = 0.2906    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2906
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8509
moved from start:          0.1813

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= 0.154
  Angle     :  0.505   9.139  14545  Z= 0.259
  Chirality :  0.038   0.136   1635
  Planarity :  0.004   0.052   1766
  Dihedral  : 12.981 169.283   1797
  Min Nonbonded Distance : 1.736

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.89 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 22.69 %
    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:  0.63 (0.24), residues: 1234
  helix:  1.72 (0.24), residues: 478
  sheet: -0.10 (0.42), residues: 147
  loop : -0.47 (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   0.004   0.000   ARG C 217 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04115 (  441)
  hydrogen bonds       : angle       4.23609 ( 1219)
  metal coordination   : bond        0.02309 (   12)
  metal coordination   : angle       3.95853 (    8)
  covalent geometry    : bond        0.00350 (10657)
  covalent geometry    : angle       0.49693 (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
  108 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 82
  time to evaluate  : 1.456 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  147 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8523 (mppt)
REVERT: A  317 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.7925 (ttm170)
REVERT: B   33 ARG cc_start: 0.8122 (mtp180) cc_final: 0.7824 (mtp180)
REVERT: B  204 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7933 (pm20)
REVERT: B  222 ASP cc_start: 0.8568 (OUTLIER) cc_final: 0.8130 (t70)
REVERT: B  475 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7391 (tmm-80)
  outliers start: 26
  outliers final: 20
  residues processed: 105
  average time/residue: 0.6300
  time to fit residues: 89.0389
Evaluate side-chains
  107 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 82
  time to evaluate  : 1.674 
-------------------------------------------------------------------------------
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  248 SER
Chi-restraints excluded: chain A residue  317 ARG
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  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  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:    0.3980
   chunk 85 optimal weight:    0.0030
   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:    0.9980
   chunk 119 optimal weight:    9.9990
   overall best weight:    0.8794

-------------------------------------------------------------------------------
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 = 0.3792 r_free = 0.3792 target = 0.147433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.102318 restraints weight = 41571.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.3160 rms_B_bonded: 2.39
r_work: 0.3033 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2921 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2921
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2921 r_free = 0.2921    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2921 r_free = 0.2921    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2921
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8497
moved from start:          0.1822

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= 0.119
  Angle     :  0.488   9.089  14545  Z= 0.249
  Chirality :  0.037   0.138   1635
  Planarity :  0.004   0.052   1766
  Dihedral  : 12.914 171.348   1797
  Min Nonbonded Distance : 1.764

Molprobity Statistics.
  All-atom Clashscore : 3.08
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.65 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 22.69 %
    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:  0.76 (0.24), residues: 1234
  helix:  1.84 (0.24), residues: 478
  sheet: -0.00 (0.43), residues: 146
  loop : -0.42 (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   0.012   0.001   PHE C 243 
 TYR   0.012   0.001   TYR A 403 
 ARG   0.004   0.000   ARG C 217 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03789 (  441)
  hydrogen bonds       : angle       4.14456 ( 1219)
  metal coordination   : bond        0.02261 (   12)
  metal coordination   : angle       3.82359 (    8)
  covalent geometry    : bond        0.00269 (10657)
  covalent geometry    : angle       0.48010 (14537)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 13112.40 seconds
wall clock time: 222 minutes 19.73 seconds (13339.73 seconds total)