Starting phenix.real_space_refine
on Thu Sep 18 09:45:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bx8_44999/09_2025/9bx8_44999_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bx8_44999/09_2025/9bx8_44999.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.59
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bx8_44999/09_2025/9bx8_44999_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bx8_44999/09_2025/9bx8_44999_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bx8_44999/09_2025/9bx8_44999.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bx8_44999/09_2025/9bx8_44999.map"
  }
  resolution = 3.59
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     Mn      4      7.51       5
     P      12      5.49       5
     Mg      2      5.21       5
     S      82      5.16       5
     C   10190      2.51       5
     N    2598      2.21       5
     O    3066      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 41 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 15954
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 5554
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 683, 5554
          Classifications: {'peptide': 683}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665}
    Chain: "B"
      Number of atoms: 5554
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 683, 5554
          Classifications: {'peptide': 683}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665}
    Chain: "C"
      Number of atoms: 2360
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 287, 2360
          Classifications: {'peptide': 287}
          Link IDs: {'PTRANS': 7, 'TRANS': 279}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 2360
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 287, 2360
          Classifications: {'peptide': 287}
          Link IDs: {'PTRANS': 7, 'TRANS': 279}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 61
          Unusual residues: {' MG': 1, 'ATP': 1, 'TTP': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 61
          Unusual residues: {' MG': 1, 'ATP': 1, 'TTP': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "C"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N   SER D 187 " occ=0.50
      ... (4 atoms not shown)
      pdb=" OG  SER D 187 " occ=0.50
    residue:
      pdb=" N   SER D 253 " occ=0.50
      ... (4 atoms not shown)
      pdb=" OG  SER D 253 " occ=0.50
    residue:
      pdb="MN    MN C 401 " occ=0.85
    residue:
      pdb="MN    MN C 402 " occ=0.85
  Time building chain proxies: 3.43, per 1000 atoms: 0.21
  Number of scatterers: 15954
  At special positions: 0
  Unit cell: (93.002, 127.75, 133.882, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Mn      4     24.99
     S      82     16.00
     P      12     15.00
     Mg      2     11.99
     O    3066      8.00
     N    2598      7.00
     C   10190      6.00
    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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.49
  Conformation dependent library (CDL) restraints added in 528.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  3856 Ramachandran restraints generated.
    1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3688

  Finding SS restraints...
    Secondary structure from input PDB file:
      99 helices and 10 sheets defined
      64.3% alpha, 6.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.47
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 15
    Processing helix  chain 'A' and resid 27 through 41
      removed outlier: 3.555A  pdb=" N   GLU A  31 " --> pdb=" O   ASP A  27 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 61
    Processing helix  chain 'A' and resid 65 through 70
      removed outlier: 4.075A  pdb=" N   LEU A  69 " --> pdb=" O   GLU A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 87
      removed outlier: 4.058A  pdb=" N   LYS A  87 " --> pdb=" O   THR A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 104
      removed outlier: 3.706A  pdb=" N   ALA A  97 " --> pdb=" O   SER A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 131
    Processing helix  chain 'A' and resid 133 through 146
    Processing helix  chain 'A' and resid 152 through 159
    Processing helix  chain 'A' and resid 178 through 195
    Processing helix  chain 'A' and resid 222 through 237
      removed outlier: 3.872A  pdb=" N   VAL A 226 " --> pdb=" O   GLY A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 242
      removed outlier: 3.793A  pdb=" N   GLN A 242 " --> pdb=" O   GLN A 239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 264
    Processing helix  chain 'A' and resid 285 through 294
      removed outlier: 3.639A  pdb=" N   VAL A 289 " --> pdb=" O   PRO A 285 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 311
    Processing helix  chain 'A' and resid 313 through 317
    Processing helix  chain 'A' and resid 318 through 329
      removed outlier: 6.056A  pdb=" N   ASP A 324 " --> pdb=" O   ASN A 320 " (cutoff:3.500A)
      removed outlier: 4.901A  pdb=" N   LYS A 325 " --> pdb=" O   GLU A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 354
    Processing helix  chain 'A' and resid 361 through 366
    Processing helix  chain 'A' and resid 416 through 423
    Processing helix  chain 'A' and resid 424 through 442
    Processing helix  chain 'A' and resid 448 through 459
    Processing helix  chain 'A' and resid 467 through 474
    Processing helix  chain 'A' and resid 481 through 511
    Processing helix  chain 'A' and resid 520 through 525
    Processing helix  chain 'A' and resid 528 through 534
    Processing helix  chain 'A' and resid 540 through 547
      removed outlier: 3.520A  pdb=" N   PHE A 547 " --> pdb=" O   ILE A 543 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 554 through 569
    Processing helix  chain 'A' and resid 583 through 589
      removed outlier: 4.274A  pdb=" N   VAL A 587 " --> pdb=" O   SER A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 628 through 632
    Processing helix  chain 'A' and resid 633 through 646
    Processing helix  chain 'A' and resid 663 through 677
    Processing helix  chain 'B' and resid 7 through 15
    Processing helix  chain 'B' and resid 27 through 41
      removed outlier: 3.548A  pdb=" N   GLU B  31 " --> pdb=" O   ASP B  27 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 61
    Processing helix  chain 'B' and resid 65 through 70
      removed outlier: 3.949A  pdb=" N   LEU B  69 " --> pdb=" O   GLU B  65 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 73 through 87
      removed outlier: 3.960A  pdb=" N   LYS B  87 " --> pdb=" O   THR B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 104
      removed outlier: 3.721A  pdb=" N   ALA B  97 " --> pdb=" O   SER B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 131
    Processing helix  chain 'B' and resid 133 through 146
    Processing helix  chain 'B' and resid 152 through 159
    Processing helix  chain 'B' and resid 178 through 195
    Processing helix  chain 'B' and resid 222 through 237
      removed outlier: 3.779A  pdb=" N   VAL B 226 " --> pdb=" O   GLY B 222 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 238 through 242
    Processing helix  chain 'B' and resid 257 through 264
    Processing helix  chain 'B' and resid 285 through 295
      removed outlier: 3.574A  pdb=" N   VAL B 289 " --> pdb=" O   PRO B 285 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 302 through 311
    Processing helix  chain 'B' and resid 313 through 317
    Processing helix  chain 'B' and resid 318 through 329
      removed outlier: 5.841A  pdb=" N   ASP B 324 " --> pdb=" O   ASN B 320 " (cutoff:3.500A)
      removed outlier: 4.622A  pdb=" N   LYS B 325 " --> pdb=" O   GLU B 321 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 354
    Processing helix  chain 'B' and resid 361 through 367
      removed outlier: 4.174A  pdb=" N   VAL B 367 " --> pdb=" O   ASN B 363 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 423
    Processing helix  chain 'B' and resid 424 through 443
    Processing helix  chain 'B' and resid 448 through 459
    Processing helix  chain 'B' and resid 467 through 474
    Processing helix  chain 'B' and resid 481 through 511
    Processing helix  chain 'B' and resid 520 through 525
    Processing helix  chain 'B' and resid 528 through 534
    Processing helix  chain 'B' and resid 540 through 547
      removed outlier: 3.566A  pdb=" N   PHE B 547 " --> pdb=" O   ILE B 543 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 554 through 569
    Processing helix  chain 'B' and resid 583 through 589
      removed outlier: 4.403A  pdb=" N   VAL B 587 " --> pdb=" O   SER B 583 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 628 through 632
    Processing helix  chain 'B' and resid 633 through 646
    Processing helix  chain 'B' and resid 663 through 677
    Processing helix  chain 'C' and resid 17 through 28
    Processing helix  chain 'C' and resid 31 through 35
    Processing helix  chain 'C' and resid 37 through 39
      No H-bonds generated for 'chain 'C' and resid 37 through 39'
    Processing helix  chain 'C' and resid 40 through 46
    Processing helix  chain 'C' and resid 48 through 72
    Processing helix  chain 'C' and resid 72 through 81
    Processing helix  chain 'C' and resid 83 through 100
    Processing helix  chain 'C' and resid 100 through 113
      removed outlier: 3.545A  pdb=" N   TYR C 105 " --> pdb=" O   HIS C 101 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   SER C 106 " --> pdb=" O   ALA C 102 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 114 through 128
      removed outlier: 3.514A  pdb=" N   LYS C 126 " --> pdb=" O   PHE C 122 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 128 through 144
    Processing helix  chain 'C' and resid 149 through 166
    Processing helix  chain 'C' and resid 168 through 180
      removed outlier: 4.935A  pdb=" N   TYR C 174 " --> pdb=" O   SER C 170 " (cutoff:3.500A)
      Proline residue:  C 175  - end of helix
    Processing helix  chain 'C' and resid 184 through 214
      removed outlier: 3.566A  pdb=" N   ILE C 200 " --> pdb=" O   ARG C 196 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 217 through 248
    Processing helix  chain 'C' and resid 249 through 251
      No H-bonds generated for 'chain 'C' and resid 249 through 251'
    Processing helix  chain 'C' and resid 252 through 271
    Processing helix  chain 'C' and resid 283 through 289
    Processing helix  chain 'C' and resid 316 through 321
    Processing helix  chain 'D' and resid 17 through 28
    Processing helix  chain 'D' and resid 31 through 35
    Processing helix  chain 'D' and resid 37 through 39
      No H-bonds generated for 'chain 'D' and resid 37 through 39'
    Processing helix  chain 'D' and resid 40 through 45
    Processing helix  chain 'D' and resid 48 through 72
    Processing helix  chain 'D' and resid 72 through 81
    Processing helix  chain 'D' and resid 83 through 100
    Processing helix  chain 'D' and resid 100 through 113
    Processing helix  chain 'D' and resid 114 through 128
    Processing helix  chain 'D' and resid 128 through 144
    Processing helix  chain 'D' and resid 149 through 166
    Processing helix  chain 'D' and resid 168 through 180
      removed outlier: 4.875A  pdb=" N   TYR D 174 " --> pdb=" O   SER D 170 " (cutoff:3.500A)
      Proline residue:  D 175  - end of helix
    Processing helix  chain 'D' and resid 184 through 214
    Processing helix  chain 'D' and resid 217 through 248
    Processing helix  chain 'D' and resid 249 through 251
      No H-bonds generated for 'chain 'D' and resid 249 through 251'
    Processing helix  chain 'D' and resid 252 through 271
    Processing helix  chain 'D' and resid 283 through 290
    Processing sheet with id=AA1, first strand: chain 'A' and resid 149 through 151
      removed outlier: 6.888A  pdb=" N   GLY A 462 " --> pdb=" O   SER A 408 " (cutoff:3.500A)
      removed outlier: 5.923A  pdb=" N   ASN A 410 " --> pdb=" O   GLY A 462 " (cutoff:3.500A)
      removed outlier: 7.139A  pdb=" N   GLY A 464 " --> pdb=" O   ASN A 410 " (cutoff:3.500A)
      removed outlier: 6.314A  pdb=" N   GLY A 412 " --> pdb=" O   GLY A 464 " (cutoff:3.500A)
      removed outlier: 7.170A  pdb=" N   MET A 466 " --> pdb=" O   GLY A 412 " (cutoff:3.500A)
      removed outlier: 6.151A  pdb=" N   LEU A 414 " --> pdb=" O   MET A 466 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151
      removed outlier: 3.736A  pdb=" N   CYS A 409 " --> pdb=" O   CYS A 170 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   CYS A 170 " --> pdb=" O   CYS A 409 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 298 through 301
    Processing sheet with id=AA4, first strand: chain 'A' and resid 601 through 606
    Processing sheet with id=AA5, first strand: chain 'A' and resid 655 through 658
    Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 151
      removed outlier: 5.890A  pdb=" N   ASN B 410 " --> pdb=" O   GLY B 462 " (cutoff:3.500A)
      removed outlier: 7.058A  pdb=" N   GLY B 464 " --> pdb=" O   ASN B 410 " (cutoff:3.500A)
      removed outlier: 6.165A  pdb=" N   GLY B 412 " --> pdb=" O   GLY B 464 " (cutoff:3.500A)
      removed outlier: 7.237A  pdb=" N   MET B 466 " --> pdb=" O   GLY B 412 " (cutoff:3.500A)
      removed outlier: 6.142A  pdb=" N   LEU B 414 " --> pdb=" O   MET B 466 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 407 through 408
      removed outlier: 6.456A  pdb=" N   GLY B 247 " --> pdb=" O   SER B 279 " (cutoff:3.500A)
      removed outlier: 7.885A  pdb=" N   GLY B 281 " --> pdb=" O   GLY B 247 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   ALA B 249 " --> pdb=" O   GLY B 281 " (cutoff:3.500A)
      removed outlier: 7.655A  pdb=" N   VAL B 283 " --> pdb=" O   ALA B 249 " (cutoff:3.500A)
      removed outlier: 6.792A  pdb=" N   LEU B 251 " --> pdb=" O   VAL B 283 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 298 through 301
    Processing sheet with id=AA9, first strand: chain 'B' and resid 601 through 606
    Processing sheet with id=AB1, first strand: chain 'B' and resid 655 through 659

    898 hydrogen bonds defined for protein.
    2616 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.74

  Time building geometry restraints manager: 1.83 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 5014
        1.34 -     1.46: 2987
        1.46 -     1.58: 8122
        1.58 -     1.70: 19
        1.70 -     1.82: 156
  Bond restraints: 16298
  Sorted by residual:
  bond pdb=" CA  VAL C 125 "
       pdb=" CB  VAL C 125 "
    ideal  model  delta    sigma   weight residual
    1.540  1.601 -0.061 1.25e-02 6.40e+03 2.37e+01
  bond pdb=" CA  ILE D 138 "
       pdb=" CB  ILE D 138 "
    ideal  model  delta    sigma   weight residual
    1.539  1.578 -0.038 1.20e-02 6.94e+03 1.01e+01
  bond pdb=" CA  VAL C 250 "
       pdb=" CB  VAL C 250 "
    ideal  model  delta    sigma   weight residual
    1.542  1.574 -0.031 1.08e-02 8.57e+03 8.31e+00
  bond pdb=" CA  ILE D  35 "
       pdb=" CB  ILE D  35 "
    ideal  model  delta    sigma   weight residual
    1.537  1.569 -0.032 1.17e-02 7.31e+03 7.53e+00
  bond pdb=" CA  VAL D 203 "
       pdb=" CB  VAL D 203 "
    ideal  model  delta    sigma   weight residual
    1.540  1.573 -0.033 1.25e-02 6.40e+03 6.76e+00
  ... (remaining 16293 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.10: 21502
        2.10 -     4.19: 465
        4.19 -     6.29: 34
        6.29 -     8.38: 1
        8.38 -    10.48: 2
  Bond angle restraints: 22004
  Sorted by residual:
  angle pdb=" N   VAL C 125 "
        pdb=" CA  VAL C 125 "
        pdb=" CB  VAL C 125 "
      ideal   model   delta    sigma   weight residual
     110.54  116.63   -6.09 1.36e+00 5.41e-01 2.00e+01
  angle pdb=" N   LEU C 167 "
        pdb=" CA  LEU C 167 "
        pdb=" C   LEU C 167 "
      ideal   model   delta    sigma   weight residual
     111.71  116.10   -4.39 1.15e+00 7.56e-01 1.46e+01
  angle pdb=" N   TYR C 247 "
        pdb=" CA  TYR C 247 "
        pdb=" C   TYR C 247 "
      ideal   model   delta    sigma   weight residual
     113.50  117.82   -4.32 1.23e+00 6.61e-01 1.23e+01
  angle pdb=" N   ASN D  38 "
        pdb=" CA  ASN D  38 "
        pdb=" C   ASN D  38 "
      ideal   model   delta    sigma   weight residual
     111.71  115.69   -3.98 1.15e+00 7.56e-01 1.20e+01
  angle pdb=" C   MET D  74 "
        pdb=" N   PRO D  75 "
        pdb=" CA  PRO D  75 "
      ideal   model   delta    sigma   weight residual
     119.19  115.55    3.64 1.06e+00 8.90e-01 1.18e+01
  ... (remaining 21999 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.32: 9428
       34.32 -    68.64: 331
       68.64 -   102.96: 47
      102.96 -   137.29: 0
      137.29 -   171.61: 2
  Dihedral angle restraints: 9808
    sinusoidal: 4062
      harmonic: 5746
  Sorted by residual:
  dihedral pdb=" C2  TTP A 801 "
           pdb=" C1' TTP A 801 "
           pdb=" N1  TTP A 801 "
           pdb=" O4' TTP A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     301.68  130.08  171.61     1      2.00e+01 2.50e-03 4.77e+01
  dihedral pdb=" C2  TTP B 801 "
           pdb=" C1' TTP B 801 "
           pdb=" N1  TTP B 801 "
           pdb=" O4' TTP B 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     301.68  135.68  166.00     1      2.00e+01 2.50e-03 4.73e+01
  dihedral pdb=" C   VAL C 125 "
           pdb=" N   VAL C 125 "
           pdb=" CA  VAL C 125 "
           pdb=" CB  VAL C 125 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -134.30   12.30     0      2.50e+00 1.60e-01 2.42e+01
  ... (remaining 9805 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.093: 2128
       0.093 -    0.186: 182
       0.186 -    0.279: 31
       0.279 -    0.372: 5
       0.372 -    0.465: 2
  Chirality restraints: 2348
  Sorted by residual:
  chirality pdb=" CA  ASN C  98 "
            pdb=" N   ASN C  98 "
            pdb=" C   ASN C  98 "
            pdb=" CB  ASN C  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.04    0.47 2.00e-01 2.50e+01 5.42e+00
  chirality pdb=" CA  TYR C 169 "
            pdb=" N   TYR C 169 "
            pdb=" C   TYR C 169 "
            pdb=" CB  TYR C 169 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.08    0.43 2.00e-01 2.50e+01 4.64e+00
  chirality pdb=" CA  TYR D 169 "
            pdb=" N   TYR D 169 "
            pdb=" C   TYR D 169 "
            pdb=" CB  TYR D 169 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.95e+00
  ... (remaining 2345 not shown)

  Planarity restraints: 2812
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B   6 "    0.036 5.00e-02 4.00e+02   5.50e-02 4.83e+00
        pdb=" N   PRO B   7 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO B   7 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B   7 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET D  74 "   -0.027 5.00e-02 4.00e+02   4.15e-02 2.75e+00
        pdb=" N   PRO D  75 "    0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO D  75 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO D  75 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE D  92 "   -0.017 2.00e-02 2.50e+03   1.11e-02 2.15e+00
        pdb=" CG  PHE D  92 "    0.020 2.00e-02 2.50e+03
        pdb=" CD1 PHE D  92 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 PHE D  92 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE D  92 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE D  92 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE D  92 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 2809 not shown)

  Histogram of nonbonded interaction distances:
        1.91 -     2.51: 132
        2.51 -     3.11: 11874
        3.11 -     3.70: 26443
        3.70 -     4.30: 41240
        4.30 -     4.90: 65005
  Nonbonded interactions: 144694
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU D  97 "
            pdb="MN    MN D 401 "
     model   vdw
     1.912 2.320
  nonbonded pdb=" O1B TTP A 801 "
            pdb="MG    MG A 802 "
     model   vdw
     1.918 2.170
  nonbonded pdb=" O2A TTP B 801 "
            pdb="MG    MG B 802 "
     model   vdw
     1.929 2.170
  nonbonded pdb=" OE2 GLU C  97 "
            pdb="MN    MN C 401 "
     model   vdw
     1.961 2.320
  nonbonded pdb=" OE2 GLU C 164 "
            pdb="MN    MN C 401 "
     model   vdw
     1.966 2.320
  ... (remaining 144689 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

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=0.43 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             1.030
  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:             0.000
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     14.570
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7142
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      :  0.008   0.833  16299  Z= 0.724
  Angle     :  0.708  10.476  22004  Z= 0.453
  Chirality :  0.059   0.465   2348
  Planarity :  0.003   0.055   2812
  Dihedral  : 17.174 171.608   6120
  Min Nonbonded Distance : 1.912

Molprobity Statistics.
  All-atom Clashscore : 17.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 14.00 %
    Favored  : 84.54 %
  Cbeta Deviations :  0.16 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.10 (0.18), residues: 1928
  helix:  1.05 (0.15), residues: 1133
  sheet:  0.46 (0.39), residues: 146
  loop :  0.45 (0.24), residues: 649

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 196 
 TYR   0.020   0.002   TYR D 179 
 PHE   0.020   0.002   PHE C 227 
 TRP   0.008   0.002   TRP D  44 
 HIS   0.006   0.001   HIS C 254 

Details of bonding type rmsd
  covalent geometry    : bond        0.00542 (16298)
  covalent geometry    : angle       0.70775 (22004)
  hydrogen bonds       : bond        0.16169 (  896)
  hydrogen bonds       : angle       6.35333 ( 2616)
  Misc. bond           : bond        0.83327 (    1)

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

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

  3856 Ramachandran restraints generated.
    1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3856 Ramachandran restraints generated.
    1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  899 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 874
  time to evaluate  : 0.601 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 ASP cc_start: 0.7281 (p0) cc_final: 0.7071 (p0)
REVERT: A  231 ASP cc_start: 0.8573 (t70) cc_final: 0.8362 (t70)
REVERT: A  259 ASN cc_start: 0.7820 (m-40) cc_final: 0.7557 (m-40)
REVERT: A  286 ASP cc_start: 0.7608 (m-30) cc_final: 0.6919 (m-30)
REVERT: A  362 ASP cc_start: 0.6787 (m-30) cc_final: 0.6355 (m-30)
REVERT: A  379 SER cc_start: 0.8842 (t) cc_final: 0.8402 (t)
REVERT: A  591 THR cc_start: 0.8603 (p) cc_final: 0.8388 (m)
REVERT: A  652 ILE cc_start: 0.9357 (mt) cc_final: 0.9058 (mt)
REVERT: A  679 ILE cc_start: 0.9348 (mm) cc_final: 0.9122 (mm)
REVERT: B   67 GLU cc_start: 0.7290 (mp0) cc_final: 0.7082 (mp0)
REVERT: B  155 THR cc_start: 0.9148 (m) cc_final: 0.8840 (t)
REVERT: B  177 ASP cc_start: 0.8411 (t0) cc_final: 0.8193 (t0)
REVERT: B  194 LYS cc_start: 0.8972 (tttt) cc_final: 0.8722 (ttpt)
REVERT: B  211 GLU cc_start: 0.7422 (mt-10) cc_final: 0.6997 (mm-30)
REVERT: B  250 TYR cc_start: 0.8678 (m-80) cc_final: 0.7882 (m-80)
REVERT: B  286 ASP cc_start: 0.7187 (m-30) cc_final: 0.6427 (m-30)
REVERT: B  357 TYR cc_start: 0.8718 (m-10) cc_final: 0.8350 (m-80)
REVERT: B  362 ASP cc_start: 0.7219 (m-30) cc_final: 0.6461 (m-30)
REVERT: B  379 SER cc_start: 0.9080 (t) cc_final: 0.8198 (t)
REVERT: B  456 LYS cc_start: 0.8749 (ttpp) cc_final: 0.8478 (ttpp)
REVERT: B  598 MET cc_start: 0.7652 (mtm) cc_final: 0.7064 (mtm)
REVERT: B  628 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7664 (mt-10)
REVERT: C   66 ASP cc_start: 0.5021 (m-30) cc_final: 0.4489 (m-30)
REVERT: C   92 PHE cc_start: 0.7840 (t80) cc_final: 0.7526 (t80)
REVERT: C  131 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6465 (mt)
REVERT: D  178 PHE cc_start: 0.5738 (m-80) cc_final: 0.5174 (m-80)
REVERT: D  213 TYR cc_start: 0.4890 (t80) cc_final: 0.4633 (t80)
REVERT: D  260 ILE cc_start: 0.7299 (mt) cc_final: 0.6411 (mp)
REVERT: D  321 TYR cc_start: 0.7759 (m-80) cc_final: 0.6593 (m-80)
  outliers start: 25
  outliers final: 4
  residues processed: 882
  average time/residue: 0.1371
  time to fit residues: 175.8553
Evaluate side-chains
  633 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 628
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 SER
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  581 THR
Chi-restraints excluded: chain C residue  125 VAL
Chi-restraints excluded: chain C residue  131 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 107 optimal weight:    0.8980
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:    7.9990
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    0.2980
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    0.0980
   chunk 91 optimal weight:    3.9990
   chunk 149 optimal weight:    0.0270
   overall best weight:    0.4640

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

Flipped N/Q/H residues before XYZ refinement:
A  11 GLN
A  14 ASN
A  19 GLN
** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 158 ASN
A 312 GLN
A 370 ASN
** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  14 ASN
** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 418 ASN
B 588 GLN
B 646 GLN
C  24 GLN
C  28 GLN
C  84 HIS
C 192 ASN
** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  80 HIS
D  91 ASN
D 127 GLN
D 136 GLN
D 233 ASN

Total number of N/Q/H flips: 19

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.147751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.103675 restraints weight = 27970.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.107592 restraints weight = 11972.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.110016 restraints weight = 6927.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.111455 restraints weight = 4863.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.112197 restraints weight = 3873.402|
|-----------------------------------------------------------------------------|
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3312
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3312 r_free = 0.3312    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3311 r_free = 0.3311    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3311
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.3675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  16299  Z= 0.150
  Angle     :  0.647  10.574  22004  Z= 0.344
  Chirality :  0.044   0.200   2348
  Planarity :  0.004   0.057   2812
  Dihedral  :  8.673 151.780   2222
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 12.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 17.97 %
    Favored  : 78.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.49 (0.18), residues: 1928
  helix:  1.39 (0.15), residues: 1132
  sheet:  1.43 (0.43), residues: 96
  loop :  0.44 (0.23), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 293 
 TYR   0.028   0.002   TYR C 173 
 PHE   0.031   0.002   PHE B 261 
 TRP   0.030   0.003   TRP C 124 
 HIS   0.021   0.001   HIS C 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 (16298)
  covalent geometry    : angle       0.64733 (22004)
  hydrogen bonds       : bond        0.04710 (  896)
  hydrogen bonds       : angle       5.17639 ( 2616)
  Misc. bond           : bond        0.00123 (    1)

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

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

  3856 Ramachandran restraints generated.
    1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3856 Ramachandran restraints generated.
    1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  756 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 698
  time to evaluate  : 0.487 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.8118 (mtpp)
REVERT: A  246 SER cc_start: 0.7325 (m) cc_final: 0.6772 (p)
REVERT: A  286 ASP cc_start: 0.8706 (m-30) cc_final: 0.7523 (m-30)
REVERT: A  312 GLN cc_start: 0.8661 (pt0) cc_final: 0.8300 (pt0)
REVERT: A  344 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7749 (mt-10)
REVERT: A  362 ASP cc_start: 0.7522 (m-30) cc_final: 0.6756 (m-30)
REVERT: A  379 SER cc_start: 0.9130 (t) cc_final: 0.8825 (t)
REVERT: A  535 ASP cc_start: 0.8175 (t0) cc_final: 0.7784 (t0)
REVERT: A  640 MET cc_start: 0.9067 (tpp) cc_final: 0.7861 (tpp)
REVERT: B  109 ASN cc_start: 0.9060 (OUTLIER) cc_final: 0.8703 (m-40)
REVERT: B  250 TYR cc_start: 0.9292 (m-80) cc_final: 0.8014 (m-80)
REVERT: B  263 ASP cc_start: 0.8855 (m-30) cc_final: 0.8510 (m-30)
REVERT: B  286 ASP cc_start: 0.8028 (m-30) cc_final: 0.7160 (m-30)
REVERT: B  321 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7501 (tm-30)
REVERT: B  334 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8727 (ptpp)
REVERT: B  355 TYR cc_start: 0.8735 (m-80) cc_final: 0.8443 (m-80)
REVERT: B  357 TYR cc_start: 0.9018 (m-10) cc_final: 0.8563 (m-80)
REVERT: B  362 ASP cc_start: 0.7822 (m-30) cc_final: 0.6674 (m-30)
REVERT: B  379 SER cc_start: 0.9301 (t) cc_final: 0.8389 (t)
REVERT: B  586 TYR cc_start: 0.8718 (m-80) cc_final: 0.8429 (m-80)
REVERT: B  598 MET cc_start: 0.8267 (mtm) cc_final: 0.7646 (mtp)
REVERT: B  599 GLU cc_start: 0.8282 (pm20) cc_final: 0.7805 (pm20)
REVERT: B  604 ARG cc_start: 0.8516 (tpp80) cc_final: 0.8064 (tpp80)
REVERT: B  628 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7644 (mm-30)
REVERT: C   42 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7497 (pp)
REVERT: C   92 PHE cc_start: 0.8334 (t80) cc_final: 0.7940 (t80)
REVERT: C   95 MET cc_start: 0.8416 (tmm) cc_final: 0.8138 (tmm)
REVERT: C   97 GLU cc_start: 0.5068 (mm-30) cc_final: 0.4165 (mm-30)
REVERT: C  122 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.8179 (m-10)
REVERT: C  183 LYS cc_start: 0.8074 (pttt) cc_final: 0.7848 (pttp)
REVERT: C  212 ILE cc_start: 0.8991 (mt) cc_final: 0.8771 (mp)
REVERT: C  213 TYR cc_start: 0.7718 (t80) cc_final: 0.7476 (t80)
REVERT: C  242 TYR cc_start: 0.8967 (t80) cc_final: 0.8515 (t80)
REVERT: C  260 ILE cc_start: 0.8140 (pt) cc_final: 0.7852 (pt)
REVERT: C  283 ASN cc_start: 0.7482 (p0) cc_final: 0.7191 (p0)
REVERT: D   17 PHE cc_start: 0.5806 (m-80) cc_final: 0.5284 (m-80)
REVERT: D   42 LEU cc_start: 0.8809 (tp) cc_final: 0.8489 (mp)
REVERT: D  117 THR cc_start: 0.8878 (m) cc_final: 0.7832 (m)
REVERT: D  119 ASN cc_start: 0.7747 (m-40) cc_final: 0.7539 (m-40)
REVERT: D  137 MET cc_start: 0.4475 (mtp) cc_final: 0.3930 (mmm)
REVERT: D  154 PHE cc_start: 0.9310 (t80) cc_final: 0.8772 (t80)
REVERT: D  157 MET cc_start: 0.9165 (mtp) cc_final: 0.8785 (ptp)
REVERT: D  213 TYR cc_start: 0.8031 (t80) cc_final: 0.7599 (t80)
REVERT: D  215 LYS cc_start: 0.8863 (mtmp) cc_final: 0.8646 (mtmm)
REVERT: D  244 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7834 (pt0)
REVERT: D  259 PHE cc_start: 0.8194 (t80) cc_final: 0.7981 (t80)
  outliers start: 58
  outliers final: 17
  residues processed: 719
  average time/residue: 0.1317
  time to fit residues: 141.4541
Evaluate side-chains
  602 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 580
  time to evaluate  : 0.666 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 SER
Chi-restraints excluded: chain A residue  107 LYS
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  399 GLU
Chi-restraints excluded: chain A residue  425 ILE
Chi-restraints excluded: chain A residue  658 LEU
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain B residue  109 ASN
Chi-restraints excluded: chain B residue  188 ILE
Chi-restraints excluded: chain B residue  334 LYS
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  584 ILE
Chi-restraints excluded: chain B residue  646 GLN
Chi-restraints excluded: chain B residue  660 ASP
Chi-restraints excluded: chain C residue   42 LEU
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue  122 PHE
Chi-restraints excluded: chain C residue  125 VAL
Chi-restraints excluded: chain C residue  196 ARG
Chi-restraints excluded: chain C residue  286 VAL
Chi-restraints excluded: chain D residue  231 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 87 optimal weight:    5.9990
   chunk 181 optimal weight:    7.9990
   chunk 149 optimal weight:    0.0870
   chunk 125 optimal weight:    3.9990
   chunk 90 optimal weight:    0.8980
   chunk 64 optimal weight:    1.9990
   chunk 156 optimal weight:    5.9990
   chunk 168 optimal weight:   10.0000
   chunk 77 optimal weight:    2.9990
   chunk 113 optimal weight:    1.9990
   overall best weight:    1.5964

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

Flipped N/Q/H residues before XYZ refinement:
A 232 ASN
A 370 ASN
A 387 GLN
** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 202 ASN
B 304 HIS
B 475 ASN
** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 186 GLN
C 263 ASN
C 265 ASN
D 127 GLN
D 210 GLN
D 233 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.140275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.097960 restraints weight = 29134.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.101488 restraints weight = 12394.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.103693 restraints weight = 7168.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.104997 restraints weight = 5060.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.105825 restraints weight = 4109.703|
|-----------------------------------------------------------------------------|
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3214
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3214 r_free = 0.3214    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3214 r_free = 0.3214    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3214
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.4471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  16299  Z= 0.185
  Angle     :  0.628   8.803  22004  Z= 0.333
  Chirality :  0.044   0.155   2348
  Planarity :  0.004   0.054   2812
  Dihedral  :  8.598 150.460   2219
  Min Nonbonded Distance : 1.885

Molprobity Statistics.
  All-atom Clashscore : 13.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 20.89 %
    Favored  : 76.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.37 (0.19), residues: 1928
  helix:  1.32 (0.15), residues: 1141
  sheet:  0.15 (0.40), residues: 144
  loop :  0.56 (0.24), residues: 643

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 196 
 TYR   0.023   0.002   TYR C 236 
 PHE   0.037   0.002   PHE D 172 
 TRP   0.024   0.002   TRP D  30 
 HIS   0.024   0.001   HIS C 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 (16298)
  covalent geometry    : angle       0.62808 (22004)
  hydrogen bonds       : bond        0.04255 (  896)
  hydrogen bonds       : angle       5.07263 ( 2616)
  Misc. bond           : bond        0.00070 (    1)

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

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

  3856 Ramachandran restraints generated.
    1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3856 Ramachandran restraints generated.
    1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  662 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 611
  time to evaluate  : 0.631 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  246 SER cc_start: 0.7189 (m) cc_final: 0.6621 (p)
REVERT: A  286 ASP cc_start: 0.8661 (m-30) cc_final: 0.7588 (m-30)
REVERT: A  344 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7722 (mt-10)
REVERT: A  355 TYR cc_start: 0.8969 (m-80) cc_final: 0.8760 (m-10)
REVERT: A  362 ASP cc_start: 0.7748 (m-30) cc_final: 0.6662 (m-30)
REVERT: A  485 ARG cc_start: 0.8448 (mtm-85) cc_final: 0.8137 (mtm-85)
REVERT: A  602 GLU cc_start: 0.7993 (tt0) cc_final: 0.6750 (tt0)
REVERT: A  604 ARG cc_start: 0.8043 (ttm110) cc_final: 0.7332 (ttm110)
REVERT: B   98 PHE cc_start: 0.9285 (t80) cc_final: 0.8822 (t80)
REVERT: B  250 TYR cc_start: 0.9387 (m-80) cc_final: 0.7898 (m-80)
REVERT: B  286 ASP cc_start: 0.8035 (m-30) cc_final: 0.7305 (m-30)
REVERT: B  318 ASP cc_start: 0.8381 (t0) cc_final: 0.7725 (t0)
REVERT: B  355 TYR cc_start: 0.8790 (m-80) cc_final: 0.8503 (m-80)
REVERT: B  362 ASP cc_start: 0.8038 (m-30) cc_final: 0.6907 (m-30)
REVERT: B  379 SER cc_start: 0.9190 (t) cc_final: 0.8431 (t)
REVERT: B  426 GLU cc_start: 0.8368 (pm20) cc_final: 0.8086 (pm20)
REVERT: B  466 MET cc_start: 0.8693 (ptm) cc_final: 0.8311 (ptm)
REVERT: B  493 MET cc_start: 0.9482 (tmm) cc_final: 0.9152 (tmm)
REVERT: B  586 TYR cc_start: 0.9166 (m-80) cc_final: 0.8479 (m-80)
REVERT: B  599 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7964 (pm20)
REVERT: B  602 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7228 (tm-30)
REVERT: B  603 GLU cc_start: 0.8174 (tp30) cc_final: 0.7544 (tp30)
REVERT: B  612 TYR cc_start: 0.8524 (m-80) cc_final: 0.6816 (m-80)
REVERT: B  628 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7869 (mt-10)
REVERT: C   37 LEU cc_start: 0.6011 (mp) cc_final: 0.5513 (mt)
REVERT: C   42 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7794 (pp)
REVERT: C   74 MET cc_start: 0.7432 (mmm) cc_final: 0.7103 (mmm)
REVERT: C   92 PHE cc_start: 0.8360 (t80) cc_final: 0.8077 (t80)
REVERT: C   95 MET cc_start: 0.8488 (tmm) cc_final: 0.8172 (tmm)
REVERT: C  105 TYR cc_start: 0.7496 (m-80) cc_final: 0.7219 (m-80)
REVERT: C  122 PHE cc_start: 0.8588 (OUTLIER) cc_final: 0.8137 (m-10)
REVERT: C  145 ILE cc_start: 0.8611 (tp) cc_final: 0.8204 (tp)
REVERT: C  227 PHE cc_start: 0.8574 (t80) cc_final: 0.8226 (t80)
REVERT: C  242 TYR cc_start: 0.9018 (t80) cc_final: 0.8739 (t80)
REVERT: C  260 ILE cc_start: 0.8379 (pt) cc_final: 0.8080 (pt)
REVERT: D   23 ASN cc_start: 0.9376 (t0) cc_final: 0.9059 (t0)
REVERT: D   27 LYS cc_start: 0.8875 (mttt) cc_final: 0.8666 (pttp)
REVERT: D   42 LEU cc_start: 0.8743 (tp) cc_final: 0.8238 (mp)
REVERT: D   46 TYR cc_start: 0.8869 (m-10) cc_final: 0.8326 (m-10)
REVERT: D  137 MET cc_start: 0.5031 (mtp) cc_final: 0.4641 (mmt)
REVERT: D  154 PHE cc_start: 0.9292 (t80) cc_final: 0.8709 (t80)
REVERT: D  169 TYR cc_start: 0.7989 (m-80) cc_final: 0.7486 (m-80)
REVERT: D  178 PHE cc_start: 0.9247 (m-80) cc_final: 0.8510 (m-80)
REVERT: D  186 GLN cc_start: 0.8637 (mm-40) cc_final: 0.8383 (mp10)
REVERT: D  193 LEU cc_start: 0.9358 (mt) cc_final: 0.8982 (mp)
REVERT: D  196 ARG cc_start: 0.8283 (ttp80) cc_final: 0.7950 (ttp80)
REVERT: D  213 TYR cc_start: 0.8365 (t80) cc_final: 0.7756 (t80)
REVERT: D  242 TYR cc_start: 0.7820 (t80) cc_final: 0.7439 (t80)
REVERT: D  244 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7990 (pt0)
REVERT: D  315 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8977 (mp)
  outliers start: 51
  outliers final: 30
  residues processed: 631
  average time/residue: 0.1332
  time to fit residues: 125.1056
Evaluate side-chains
  575 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 541
  time to evaluate  : 0.636 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 SER
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  425 ILE
Chi-restraints excluded: chain A residue  433 THR
Chi-restraints excluded: chain A residue  440 SER
Chi-restraints excluded: chain A residue  611 THR
Chi-restraints excluded: chain A residue  653 SER
Chi-restraints excluded: chain A residue  658 LEU
Chi-restraints excluded: chain A residue  661 THR
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain B residue  188 ILE
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  421 GLU
Chi-restraints excluded: chain B residue  460 SER
Chi-restraints excluded: chain B residue  584 ILE
Chi-restraints excluded: chain B residue  599 GLU
Chi-restraints excluded: chain B residue  605 THR
Chi-restraints excluded: chain B residue  658 LEU
Chi-restraints excluded: chain B residue  660 ASP
Chi-restraints excluded: chain C residue   42 LEU
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue  122 PHE
Chi-restraints excluded: chain C residue  125 VAL
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain C residue  196 ARG
Chi-restraints excluded: chain D residue   59 LEU
Chi-restraints excluded: chain D residue   76 ILE
Chi-restraints excluded: chain D residue  130 TYR
Chi-restraints excluded: chain D residue  189 GLU
Chi-restraints excluded: chain D residue  315 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 93 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9980
   chunk 147 optimal weight:    5.9990
   chunk 132 optimal weight:    0.9980
   chunk 185 optimal weight:    9.9990
   chunk 89 optimal weight:    3.9990
   chunk 54 optimal weight:    5.9990
   chunk 145 optimal weight:    6.9990
   chunk 172 optimal weight:    2.9990
   chunk 134 optimal weight:    0.6980
   chunk 171 optimal weight:    8.9990
   overall best weight:    1.9384

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

Flipped N/Q/H residues before XYZ refinement:
** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 668 ASN
B  44 ASN
B 131 ASN
B 304 HIS
B 474 GLN
B 568 HIS
** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 263 ASN
D 210 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.136335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.093061 restraints weight = 28983.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.096583 restraints weight = 12464.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.098775 restraints weight = 7235.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.100081 restraints weight = 5143.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.100904 restraints weight = 4168.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3152
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3152 r_free = 0.3152    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3152 r_free = 0.3152    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3152
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.5061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  16299  Z= 0.202
  Angle     :  0.639  11.401  22004  Z= 0.337
  Chirality :  0.044   0.164   2348
  Planarity :  0.004   0.054   2812
  Dihedral  :  8.583 147.059   2218
  Min Nonbonded Distance : 1.870

Molprobity Statistics.
  All-atom Clashscore : 14.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 20.60 %
    Favored  : 74.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.29 (0.19), residues: 1928
  helix:  1.30 (0.15), residues: 1128
  sheet: -0.24 (0.40), residues: 152
  loop :  0.56 (0.24), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 235 
 TYR   0.021   0.001   TYR D 236 
 PHE   0.034   0.002   PHE D 172 
 TRP   0.023   0.002   TRP D  30 
 HIS   0.024   0.001   HIS C 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00454 (16298)
  covalent geometry    : angle       0.63893 (22004)
  hydrogen bonds       : bond        0.04087 (  896)
  hydrogen bonds       : angle       5.05577 ( 2616)
  Misc. bond           : bond        0.00062 (    1)

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

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

  3856 Ramachandran restraints generated.
    1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3856 Ramachandran restraints generated.
    1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  662 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 586
  time to evaluate  : 0.659 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  228 LYS cc_start: 0.8901 (mtpp) cc_final: 0.8670 (mmtt)
REVERT: A  246 SER cc_start: 0.7146 (m) cc_final: 0.6654 (p)
REVERT: A  286 ASP cc_start: 0.8648 (m-30) cc_final: 0.7725 (m-30)
REVERT: A  344 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7819 (mt-10)
REVERT: A  362 ASP cc_start: 0.7825 (m-30) cc_final: 0.6719 (m-30)
REVERT: A  384 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.6268 (pm20)
REVERT: A  485 ARG cc_start: 0.8493 (mtm-85) cc_final: 0.7949 (mtm-85)
REVERT: A  570 MET cc_start: 0.8753 (mtp) cc_final: 0.8403 (mtp)
REVERT: A  586 TYR cc_start: 0.9048 (m-80) cc_final: 0.8711 (m-10)
REVERT: A  602 GLU cc_start: 0.8044 (tt0) cc_final: 0.6803 (tt0)
REVERT: A  604 ARG cc_start: 0.8153 (ttm110) cc_final: 0.7429 (ttm110)
REVERT: A  639 ASP cc_start: 0.8528 (OUTLIER) cc_final: 0.8251 (m-30)
REVERT: B   98 PHE cc_start: 0.9340 (t80) cc_final: 0.8770 (t80)
REVERT: B  109 ASN cc_start: 0.9124 (OUTLIER) cc_final: 0.8749 (m-40)
REVERT: B  250 TYR cc_start: 0.9439 (m-80) cc_final: 0.7695 (m-80)
REVERT: B  263 ASP cc_start: 0.8776 (m-30) cc_final: 0.8395 (m-30)
REVERT: B  286 ASP cc_start: 0.8136 (m-30) cc_final: 0.7537 (m-30)
REVERT: B  355 TYR cc_start: 0.8784 (m-80) cc_final: 0.8508 (m-80)
REVERT: B  362 ASP cc_start: 0.8046 (m-30) cc_final: 0.6726 (m-30)
REVERT: B  379 SER cc_start: 0.9175 (t) cc_final: 0.8361 (t)
REVERT: B  586 TYR cc_start: 0.9126 (m-80) cc_final: 0.8566 (m-80)
REVERT: B  599 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.8034 (pm20)
REVERT: B  602 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7113 (tm-30)
REVERT: B  603 GLU cc_start: 0.8276 (tp30) cc_final: 0.7714 (tp30)
REVERT: B  612 TYR cc_start: 0.8741 (m-80) cc_final: 0.7287 (m-80)
REVERT: B  624 PHE cc_start: 0.8795 (t80) cc_final: 0.8493 (t80)
REVERT: B  625 PHE cc_start: 0.9160 (m-10) cc_final: 0.8859 (m-80)
REVERT: B  628 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7867 (mt-10)
REVERT: C   20 MET cc_start: 0.8280 (tpt) cc_final: 0.7153 (ptp)
REVERT: C   21 PHE cc_start: 0.8980 (OUTLIER) cc_final: 0.8452 (t80)
REVERT: C   74 MET cc_start: 0.7777 (mmm) cc_final: 0.7425 (mmm)
REVERT: C   92 PHE cc_start: 0.8578 (t80) cc_final: 0.8201 (t80)
REVERT: C   95 MET cc_start: 0.8588 (tmm) cc_final: 0.8254 (tmm)
REVERT: C  105 TYR cc_start: 0.7850 (m-80) cc_final: 0.7435 (m-80)
REVERT: C  122 PHE cc_start: 0.8515 (OUTLIER) cc_final: 0.8071 (m-10)
REVERT: C  178 PHE cc_start: 0.9198 (m-10) cc_final: 0.8371 (m-10)
REVERT: C  183 LYS cc_start: 0.7980 (pttm) cc_final: 0.6272 (ttmt)
REVERT: C  204 TYR cc_start: 0.7900 (t80) cc_final: 0.7465 (t80)
REVERT: C  227 PHE cc_start: 0.8694 (t80) cc_final: 0.8273 (t80)
REVERT: C  231 LEU cc_start: 0.9320 (mm) cc_final: 0.8806 (pp)
REVERT: C  242 TYR cc_start: 0.9251 (t80) cc_final: 0.8672 (t80)
REVERT: C  246 LEU cc_start: 0.9141 (mm) cc_final: 0.8788 (pp)
REVERT: D   17 PHE cc_start: 0.5463 (m-80) cc_final: 0.5161 (m-80)
REVERT: D   42 LEU cc_start: 0.8702 (tp) cc_final: 0.8406 (mp)
REVERT: D   56 MET cc_start: 0.7238 (mmm) cc_final: 0.6860 (ptp)
REVERT: D  137 MET cc_start: 0.5360 (mtp) cc_final: 0.4877 (mmt)
REVERT: D  154 PHE cc_start: 0.9285 (t80) cc_final: 0.8736 (t80)
REVERT: D  178 PHE cc_start: 0.9301 (m-80) cc_final: 0.8681 (m-80)
REVERT: D  186 GLN cc_start: 0.8568 (mm-40) cc_final: 0.8315 (mp10)
REVERT: D  213 TYR cc_start: 0.8503 (t80) cc_final: 0.7680 (t80)
REVERT: D  225 ARG cc_start: 0.9160 (mtm-85) cc_final: 0.8696 (mtm180)
REVERT: D  233 ASN cc_start: 0.8186 (m-40) cc_final: 0.7978 (m110)
REVERT: D  236 TYR cc_start: 0.7758 (t80) cc_final: 0.7261 (t80)
  outliers start: 76
  outliers final: 40
  residues processed: 621
  average time/residue: 0.1326
  time to fit residues: 122.6523
Evaluate side-chains
  578 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 532
  time to evaluate  : 0.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  227 MET
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  351 SER
Chi-restraints excluded: chain A residue  384 GLU
Chi-restraints excluded: chain A residue  425 ILE
Chi-restraints excluded: chain A residue  433 THR
Chi-restraints excluded: chain A residue  440 SER
Chi-restraints excluded: chain A residue  611 THR
Chi-restraints excluded: chain A residue  639 ASP
Chi-restraints excluded: chain A residue  653 SER
Chi-restraints excluded: chain A residue  661 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   96 SER
Chi-restraints excluded: chain B residue  109 ASN
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  410 ASN
Chi-restraints excluded: chain B residue  421 GLU
Chi-restraints excluded: chain B residue  435 SER
Chi-restraints excluded: chain B residue  440 SER
Chi-restraints excluded: chain B residue  441 GLU
Chi-restraints excluded: chain B residue  460 SER
Chi-restraints excluded: chain B residue  584 ILE
Chi-restraints excluded: chain B residue  599 GLU
Chi-restraints excluded: chain B residue  658 LEU
Chi-restraints excluded: chain B residue  660 ASP
Chi-restraints excluded: chain C residue   21 PHE
Chi-restraints excluded: chain C residue  122 PHE
Chi-restraints excluded: chain C residue  174 TYR
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain C residue  196 ARG
Chi-restraints excluded: chain D residue   41 LEU
Chi-restraints excluded: chain D residue   76 ILE
Chi-restraints excluded: chain D residue  106 SER
Chi-restraints excluded: chain D residue  130 TYR
Chi-restraints excluded: chain D residue  189 GLU
Chi-restraints excluded: chain D residue  200 ILE
Chi-restraints excluded: chain D residue  211 GLU
Chi-restraints excluded: chain D residue  231 LEU
Chi-restraints excluded: chain D residue  243 THR
Chi-restraints excluded: chain D residue  250 VAL
Chi-restraints excluded: chain D residue  282 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 191 optimal weight:    5.9990
   chunk 19 optimal weight:    0.7980
   chunk 102 optimal weight:    0.9980
   chunk 164 optimal weight:    1.9990
   chunk 189 optimal weight:    6.9990
   chunk 31 optimal weight:    0.9980
   chunk 145 optimal weight:    1.9990
   chunk 107 optimal weight:    6.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 646 GLN
B 131 ASN
** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  28 GLN
D 216 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.139696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.097064 restraints weight = 28913.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.100720 restraints weight = 12086.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.102928 restraints weight = 7017.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.104187 restraints weight = 4977.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 50)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.104988 restraints weight = 4066.648|
|-----------------------------------------------------------------------------|
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3211
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3211 r_free = 0.3211    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3211 r_free = 0.3211    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3211
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.5385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  16299  Z= 0.164
  Angle     :  0.633  12.283  22004  Z= 0.332
  Chirality :  0.044   0.191   2348
  Planarity :  0.004   0.052   2812
  Dihedral  :  8.509 144.662   2216
  Min Nonbonded Distance : 1.896

Molprobity Statistics.
  All-atom Clashscore : 13.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 22.75 %
    Favored  : 73.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.11 (0.19), residues: 1928
  helix:  1.20 (0.15), residues: 1147
  sheet: -0.43 (0.40), residues: 152
  loop :  0.40 (0.24), residues: 629

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 225 
 TYR   0.026   0.002   TYR D 242 
 PHE   0.031   0.002   PHE D 172 
 TRP   0.027   0.002   TRP D  30 
 HIS   0.025   0.001   HIS C 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 (16298)
  covalent geometry    : angle       0.63337 (22004)
  hydrogen bonds       : bond        0.03881 (  896)
  hydrogen bonds       : angle       5.05721 ( 2616)
  Misc. bond           : bond        0.00042 (    1)

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

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

  3856 Ramachandran restraints generated.
    1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3856 Ramachandran restraints generated.
    1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  652 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 590
  time to evaluate  : 0.656 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  228 LYS cc_start: 0.8937 (mtpp) cc_final: 0.8686 (mmtt)
REVERT: A  266 LYS cc_start: 0.9017 (mttp) cc_final: 0.8728 (mttp)
REVERT: A  286 ASP cc_start: 0.8669 (m-30) cc_final: 0.7800 (m-30)
REVERT: A  344 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7652 (mt-10)
REVERT: A  362 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.6672 (m-30)
REVERT: A  485 ARG cc_start: 0.8511 (mtm-85) cc_final: 0.8229 (mtm-85)
REVERT: A  639 ASP cc_start: 0.8452 (OUTLIER) cc_final: 0.8168 (m-30)
REVERT: A  684 TYR cc_start: 0.8387 (OUTLIER) cc_final: 0.7731 (m-80)
REVERT: A  688 LYS cc_start: 0.7173 (pptt) cc_final: 0.6896 (pptt)
REVERT: B   98 PHE cc_start: 0.9328 (t80) cc_final: 0.8705 (t80)
REVERT: B  109 ASN cc_start: 0.9015 (OUTLIER) cc_final: 0.7787 (m-40)
REVERT: B  250 TYR cc_start: 0.9392 (m-80) cc_final: 0.7486 (m-80)
REVERT: B  286 ASP cc_start: 0.8097 (m-30) cc_final: 0.7327 (m-30)
REVERT: B  355 TYR cc_start: 0.8671 (m-80) cc_final: 0.8399 (m-80)
REVERT: B  357 TYR cc_start: 0.8976 (m-10) cc_final: 0.8643 (m-80)
REVERT: B  362 ASP cc_start: 0.8005 (m-30) cc_final: 0.6576 (m-30)
REVERT: B  379 SER cc_start: 0.9142 (t) cc_final: 0.8291 (t)
REVERT: B  529 ASP cc_start: 0.8238 (m-30) cc_final: 0.7720 (m-30)
REVERT: B  586 TYR cc_start: 0.9161 (m-80) cc_final: 0.8537 (m-80)
REVERT: B  599 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.8028 (pm20)
REVERT: B  602 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7655 (tm-30)
REVERT: B  612 TYR cc_start: 0.8572 (m-80) cc_final: 0.7849 (m-80)
REVERT: B  628 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7922 (mt-10)
REVERT: B  668 ASN cc_start: 0.8645 (m-40) cc_final: 0.7952 (m110)
REVERT: C   21 PHE cc_start: 0.9047 (OUTLIER) cc_final: 0.8306 (t80)
REVERT: C   40 ASP cc_start: 0.8642 (p0) cc_final: 0.8201 (p0)
REVERT: C   44 TRP cc_start: 0.7797 (t-100) cc_final: 0.7503 (t-100)
REVERT: C   82 ASP cc_start: 0.8569 (m-30) cc_final: 0.7952 (p0)
REVERT: C   95 MET cc_start: 0.8628 (tmm) cc_final: 0.8268 (tmm)
REVERT: C  105 TYR cc_start: 0.7944 (m-80) cc_final: 0.7562 (m-80)
REVERT: C  122 PHE cc_start: 0.8457 (OUTLIER) cc_final: 0.8047 (m-10)
REVERT: C  174 TYR cc_start: 0.7490 (OUTLIER) cc_final: 0.7071 (t80)
REVERT: C  178 PHE cc_start: 0.9034 (m-10) cc_final: 0.8531 (m-10)
REVERT: C  227 PHE cc_start: 0.8713 (t80) cc_final: 0.8480 (t80)
REVERT: C  233 ASN cc_start: 0.8855 (m110) cc_final: 0.8364 (p0)
REVERT: C  242 TYR cc_start: 0.9233 (t80) cc_final: 0.8715 (t80)
REVERT: C  246 LEU cc_start: 0.9173 (mm) cc_final: 0.8830 (pp)
REVERT: D   17 PHE cc_start: 0.5572 (m-80) cc_final: 0.5175 (m-80)
REVERT: D   46 TYR cc_start: 0.8884 (m-10) cc_final: 0.8665 (m-10)
REVERT: D  131 LEU cc_start: 0.7685 (tp) cc_final: 0.7336 (tt)
REVERT: D  137 MET cc_start: 0.5739 (mtp) cc_final: 0.5330 (mmt)
REVERT: D  154 PHE cc_start: 0.9286 (t80) cc_final: 0.8797 (t80)
REVERT: D  178 PHE cc_start: 0.9273 (m-80) cc_final: 0.8809 (m-80)
REVERT: D  186 GLN cc_start: 0.8612 (mm110) cc_final: 0.8347 (mp10)
REVERT: D  233 ASN cc_start: 0.8327 (m-40) cc_final: 0.8102 (m110)
REVERT: D  236 TYR cc_start: 0.7808 (t80) cc_final: 0.7358 (t80)
REVERT: D  263 ASN cc_start: 0.8468 (p0) cc_final: 0.8154 (p0)
REVERT: D  315 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8841 (mt)
  outliers start: 62
  outliers final: 39
  residues processed: 611
  average time/residue: 0.1300
  time to fit residues: 119.0816
Evaluate side-chains
  575 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 527
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  351 SER
Chi-restraints excluded: chain A residue  362 ASP
Chi-restraints excluded: chain A residue  425 ILE
Chi-restraints excluded: chain A residue  440 SER
Chi-restraints excluded: chain A residue  589 SER
Chi-restraints excluded: chain A residue  639 ASP
Chi-restraints excluded: chain A residue  653 SER
Chi-restraints excluded: chain A residue  661 THR
Chi-restraints excluded: chain A residue  684 TYR
Chi-restraints excluded: chain B residue  109 ASN
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  410 ASN
Chi-restraints excluded: chain B residue  435 SER
Chi-restraints excluded: chain B residue  440 SER
Chi-restraints excluded: chain B residue  441 GLU
Chi-restraints excluded: chain B residue  460 SER
Chi-restraints excluded: chain B residue  584 ILE
Chi-restraints excluded: chain B residue  599 GLU
Chi-restraints excluded: chain B residue  658 LEU
Chi-restraints excluded: chain B residue  660 ASP
Chi-restraints excluded: chain C residue   21 PHE
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain C residue   42 LEU
Chi-restraints excluded: chain C residue   81 VAL
Chi-restraints excluded: chain C residue  108 ILE
Chi-restraints excluded: chain C residue  122 PHE
Chi-restraints excluded: chain C residue  174 TYR
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain C residue  196 ARG
Chi-restraints excluded: chain C residue  256 VAL
Chi-restraints excluded: chain D residue   41 LEU
Chi-restraints excluded: chain D residue   76 ILE
Chi-restraints excluded: chain D residue  106 SER
Chi-restraints excluded: chain D residue  130 TYR
Chi-restraints excluded: chain D residue  189 GLU
Chi-restraints excluded: chain D residue  195 LEU
Chi-restraints excluded: chain D residue  200 ILE
Chi-restraints excluded: chain D residue  215 LYS
Chi-restraints excluded: chain D residue  250 VAL
Chi-restraints excluded: chain D residue  282 ILE
Chi-restraints excluded: chain D residue  315 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 92 optimal weight:    5.9990
   chunk 14 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 82 optimal weight:    0.6980
   chunk 125 optimal weight:    2.9990
   chunk 72 optimal weight:    4.9990
   chunk 84 optimal weight:    3.9990
   chunk 86 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.139166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.096640 restraints weight = 28612.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.100179 restraints weight = 11949.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.102321 restraints weight = 6989.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.103584 restraints weight = 4983.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.104153 restraints weight = 4070.008|
|-----------------------------------------------------------------------------|
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3198
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3198 r_free = 0.3198    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3198 r_free = 0.3198    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3198
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.5670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  16299  Z= 0.174
  Angle     :  0.655  12.562  22004  Z= 0.340
  Chirality :  0.045   0.242   2348
  Planarity :  0.004   0.052   2812
  Dihedral  :  8.487 144.372   2216
  Min Nonbonded Distance : 1.891

Molprobity Statistics.
  All-atom Clashscore : 14.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 24.50 %
    Favored  : 71.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.03 (0.19), residues: 1928
  helix:  1.12 (0.15), residues: 1145
  sheet: -0.47 (0.40), residues: 152
  loop :  0.42 (0.24), residues: 631

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 225 
 TYR   0.022   0.001   TYR C 142 
 PHE   0.029   0.002   PHE D 172 
 TRP   0.028   0.002   TRP D  30 
 HIS   0.025   0.001   HIS C 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 (16298)
  covalent geometry    : angle       0.65486 (22004)
  hydrogen bonds       : bond        0.03877 (  896)
  hydrogen bonds       : angle       5.10403 ( 2616)
  Misc. bond           : bond        0.00042 (    1)

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

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

  3856 Ramachandran restraints generated.
    1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3856 Ramachandran restraints generated.
    1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  627 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 563
  time to evaluate  : 0.751 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  228 LYS cc_start: 0.8957 (mtpp) cc_final: 0.8708 (mmtt)
REVERT: A  286 ASP cc_start: 0.8667 (m-30) cc_final: 0.7773 (m-30)
REVERT: A  344 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7738 (mt-10)
REVERT: A  362 ASP cc_start: 0.7695 (OUTLIER) cc_final: 0.6665 (m-30)
REVERT: A  485 ARG cc_start: 0.8512 (mtm-85) cc_final: 0.8219 (mtm110)
REVERT: A  570 MET cc_start: 0.8771 (mtp) cc_final: 0.8491 (mtp)
REVERT: A  639 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.8140 (m-30)
REVERT: A  684 TYR cc_start: 0.8380 (OUTLIER) cc_final: 0.7782 (m-80)
REVERT: B   98 PHE cc_start: 0.9351 (t80) cc_final: 0.8696 (t80)
REVERT: B  109 ASN cc_start: 0.8880 (OUTLIER) cc_final: 0.8549 (m-40)
REVERT: B  121 ARG cc_start: 0.9313 (OUTLIER) cc_final: 0.8778 (tpt170)
REVERT: B  167 LEU cc_start: 0.9090 (mt) cc_final: 0.8589 (mp)
REVERT: B  250 TYR cc_start: 0.9408 (m-80) cc_final: 0.7500 (m-80)
REVERT: B  286 ASP cc_start: 0.8056 (m-30) cc_final: 0.7443 (m-30)
REVERT: B  317 MET cc_start: 0.8474 (mtp) cc_final: 0.7899 (mtp)
REVERT: B  355 TYR cc_start: 0.8685 (m-80) cc_final: 0.8432 (m-80)
REVERT: B  357 TYR cc_start: 0.9032 (m-10) cc_final: 0.8734 (m-80)
REVERT: B  362 ASP cc_start: 0.8009 (m-30) cc_final: 0.6500 (m-30)
REVERT: B  379 SER cc_start: 0.9126 (t) cc_final: 0.8348 (t)
REVERT: B  586 TYR cc_start: 0.8942 (m-80) cc_final: 0.8530 (m-80)
REVERT: B  612 TYR cc_start: 0.8620 (m-80) cc_final: 0.8014 (m-80)
REVERT: B  628 GLU cc_start: 0.8373 (mt-10) cc_final: 0.7976 (mt-10)
REVERT: B  668 ASN cc_start: 0.8574 (m-40) cc_final: 0.8272 (m110)
REVERT: C   21 PHE cc_start: 0.8952 (OUTLIER) cc_final: 0.8237 (t80)
REVERT: C   25 ASN cc_start: 0.8966 (OUTLIER) cc_final: 0.8598 (p0)
REVERT: C   40 ASP cc_start: 0.8758 (p0) cc_final: 0.8042 (p0)
REVERT: C   92 PHE cc_start: 0.8520 (t80) cc_final: 0.7995 (t80)
REVERT: C   95 MET cc_start: 0.8847 (tmm) cc_final: 0.8544 (tmm)
REVERT: C  105 TYR cc_start: 0.7957 (m-80) cc_final: 0.7616 (m-80)
REVERT: C  122 PHE cc_start: 0.8473 (OUTLIER) cc_final: 0.8075 (m-10)
REVERT: C  149 ASP cc_start: 0.8602 (t0) cc_final: 0.8363 (t0)
REVERT: C  178 PHE cc_start: 0.8993 (m-10) cc_final: 0.8147 (m-10)
REVERT: C  183 LYS cc_start: 0.7774 (pttm) cc_final: 0.5802 (ttmt)
REVERT: C  233 ASN cc_start: 0.8878 (m110) cc_final: 0.8498 (p0)
REVERT: C  242 TYR cc_start: 0.9195 (t80) cc_final: 0.8760 (t80)
REVERT: C  245 ASP cc_start: 0.9308 (t0) cc_final: 0.8915 (m-30)
REVERT: C  270 ASN cc_start: 0.8778 (m-40) cc_final: 0.8539 (m-40)
REVERT: C  276 TYR cc_start: 0.7946 (t80) cc_final: 0.7719 (t80)
REVERT: D   46 TYR cc_start: 0.8928 (m-10) cc_final: 0.8634 (m-10)
REVERT: D  137 MET cc_start: 0.6158 (mtp) cc_final: 0.5712 (mmt)
REVERT: D  154 PHE cc_start: 0.9338 (t80) cc_final: 0.8843 (t80)
REVERT: D  169 TYR cc_start: 0.8683 (m-80) cc_final: 0.8111 (m-80)
REVERT: D  178 PHE cc_start: 0.9303 (m-80) cc_final: 0.9033 (m-80)
REVERT: D  181 GLN cc_start: 0.8479 (mt0) cc_final: 0.8213 (mp10)
REVERT: D  186 GLN cc_start: 0.8573 (mm110) cc_final: 0.8316 (mp10)
REVERT: D  213 TYR cc_start: 0.9016 (t80) cc_final: 0.8706 (t80)
REVERT: D  224 LEU cc_start: 0.9261 (pp) cc_final: 0.9009 (pp)
REVERT: D  236 TYR cc_start: 0.7938 (t80) cc_final: 0.7685 (t80)
REVERT: D  263 ASN cc_start: 0.8569 (p0) cc_final: 0.8212 (p0)
REVERT: D  315 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8830 (mt)
  outliers start: 64
  outliers final: 39
  residues processed: 590
  average time/residue: 0.1289
  time to fit residues: 113.6218
Evaluate side-chains
  574 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 526
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  351 SER
Chi-restraints excluded: chain A residue  362 ASP
Chi-restraints excluded: chain A residue  425 ILE
Chi-restraints excluded: chain A residue  435 SER
Chi-restraints excluded: chain A residue  440 SER
Chi-restraints excluded: chain A residue  639 ASP
Chi-restraints excluded: chain A residue  653 SER
Chi-restraints excluded: chain A residue  658 LEU
Chi-restraints excluded: chain A residue  684 TYR
Chi-restraints excluded: chain B residue  109 ASN
Chi-restraints excluded: chain B residue  121 ARG
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  410 ASN
Chi-restraints excluded: chain B residue  435 SER
Chi-restraints excluded: chain B residue  441 GLU
Chi-restraints excluded: chain B residue  460 SER
Chi-restraints excluded: chain B residue  494 MET
Chi-restraints excluded: chain B residue  584 ILE
Chi-restraints excluded: chain B residue  658 LEU
Chi-restraints excluded: chain B residue  660 ASP
Chi-restraints excluded: chain C residue   21 PHE
Chi-restraints excluded: chain C residue   25 ASN
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain C residue   81 VAL
Chi-restraints excluded: chain C residue  108 ILE
Chi-restraints excluded: chain C residue  122 PHE
Chi-restraints excluded: chain C residue  174 TYR
Chi-restraints excluded: chain C residue  196 ARG
Chi-restraints excluded: chain C residue  256 VAL
Chi-restraints excluded: chain D residue   41 LEU
Chi-restraints excluded: chain D residue   76 ILE
Chi-restraints excluded: chain D residue  106 SER
Chi-restraints excluded: chain D residue  130 TYR
Chi-restraints excluded: chain D residue  189 GLU
Chi-restraints excluded: chain D residue  195 LEU
Chi-restraints excluded: chain D residue  200 ILE
Chi-restraints excluded: chain D residue  211 GLU
Chi-restraints excluded: chain D residue  250 VAL
Chi-restraints excluded: chain D residue  282 ILE
Chi-restraints excluded: chain D residue  315 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 2 optimal weight:    7.9990
   chunk 165 optimal weight:    0.7980
   chunk 32 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 147 optimal weight:    6.9990
   chunk 21 optimal weight:    0.8980
   chunk 46 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 100 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  25 ASN
** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.140658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.098279 restraints weight = 28408.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.101900 restraints weight = 11959.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.104078 restraints weight = 6920.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.105314 restraints weight = 4926.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.106056 restraints weight = 4036.965|
|-----------------------------------------------------------------------------|
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3234
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3234 r_free = 0.3234    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3234 r_free = 0.3234    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3234
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.5914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  16299  Z= 0.141
  Angle     :  0.658  13.220  22004  Z= 0.341
  Chirality :  0.044   0.248   2348
  Planarity :  0.003   0.050   2812
  Dihedral  :  8.344 140.991   2216
  Min Nonbonded Distance : 1.940

Molprobity Statistics.
  All-atom Clashscore : 13.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 25.67 %
    Favored  : 71.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.99 (0.19), residues: 1928
  helix:  1.12 (0.15), residues: 1136
  sheet: -0.27 (0.41), residues: 140
  loop :  0.27 (0.24), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 117 
 TYR   0.031   0.001   TYR C 247 
 PHE   0.048   0.002   PHE D 227 
 TRP   0.029   0.002   TRP D  30 
 HIS   0.028   0.001   HIS C 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 (16298)
  covalent geometry    : angle       0.65807 (22004)
  hydrogen bonds       : bond        0.03775 (  896)
  hydrogen bonds       : angle       5.08174 ( 2616)
  Misc. bond           : bond        0.00028 (    1)

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

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

  3856 Ramachandran restraints generated.
    1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3856 Ramachandran restraints generated.
    1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  604 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 554
  time to evaluate  : 0.667 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ASN cc_start: 0.8833 (m-40) cc_final: 0.8383 (t0)
REVERT: A  228 LYS cc_start: 0.8989 (mtpp) cc_final: 0.8740 (mmtt)
REVERT: A  266 LYS cc_start: 0.8933 (mttp) cc_final: 0.8713 (mttp)
REVERT: A  286 ASP cc_start: 0.8665 (m-30) cc_final: 0.7811 (m-30)
REVERT: A  344 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7673 (mt-10)
REVERT: A  355 TYR cc_start: 0.8906 (m-80) cc_final: 0.8483 (m-80)
REVERT: A  362 ASP cc_start: 0.7662 (OUTLIER) cc_final: 0.6653 (m-30)
REVERT: A  485 ARG cc_start: 0.8507 (mtm-85) cc_final: 0.7959 (mtm-85)
REVERT: A  570 MET cc_start: 0.8775 (mtp) cc_final: 0.8495 (mtp)
REVERT: A  639 ASP cc_start: 0.8464 (OUTLIER) cc_final: 0.8126 (m-30)
REVERT: A  684 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.7796 (m-80)
REVERT: B   98 PHE cc_start: 0.9284 (t80) cc_final: 0.8596 (t80)
REVERT: B  109 ASN cc_start: 0.8826 (OUTLIER) cc_final: 0.8508 (m-40)
REVERT: B  121 ARG cc_start: 0.9282 (OUTLIER) cc_final: 0.8794 (tpt170)
REVERT: B  250 TYR cc_start: 0.9374 (m-80) cc_final: 0.7480 (m-80)
REVERT: B  263 ASP cc_start: 0.8754 (m-30) cc_final: 0.8297 (m-30)
REVERT: B  286 ASP cc_start: 0.8080 (m-30) cc_final: 0.7337 (m-30)
REVERT: B  317 MET cc_start: 0.8448 (mtp) cc_final: 0.7932 (mtp)
REVERT: B  355 TYR cc_start: 0.8592 (m-80) cc_final: 0.8362 (m-80)
REVERT: B  357 TYR cc_start: 0.8965 (m-10) cc_final: 0.8652 (m-80)
REVERT: B  362 ASP cc_start: 0.7991 (m-30) cc_final: 0.6578 (m-30)
REVERT: B  379 SER cc_start: 0.9077 (t) cc_final: 0.8245 (t)
REVERT: B  529 ASP cc_start: 0.8033 (m-30) cc_final: 0.7799 (m-30)
REVERT: B  586 TYR cc_start: 0.8980 (m-80) cc_final: 0.8588 (m-80)
REVERT: B  602 GLU cc_start: 0.7699 (tm-30) cc_final: 0.7495 (tm-30)
REVERT: B  603 GLU cc_start: 0.8377 (tp30) cc_final: 0.7980 (tp30)
REVERT: B  610 LYS cc_start: 0.8445 (tppt) cc_final: 0.7876 (tptp)
REVERT: B  612 TYR cc_start: 0.8516 (m-80) cc_final: 0.7893 (m-80)
REVERT: B  615 MET cc_start: 0.9172 (mmm) cc_final: 0.8610 (mmp)
REVERT: B  628 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7978 (mt-10)
REVERT: B  668 ASN cc_start: 0.8639 (m-40) cc_final: 0.7913 (m110)
REVERT: C   21 PHE cc_start: 0.8824 (OUTLIER) cc_final: 0.8266 (t80)
REVERT: C   40 ASP cc_start: 0.8785 (p0) cc_final: 0.8306 (p0)
REVERT: C   44 TRP cc_start: 0.7795 (t-100) cc_final: 0.7343 (t-100)
REVERT: C   95 MET cc_start: 0.8787 (tmm) cc_final: 0.8581 (tmm)
REVERT: C  105 TYR cc_start: 0.8119 (m-80) cc_final: 0.7810 (m-80)
REVERT: C  134 LYS cc_start: 0.9308 (pttt) cc_final: 0.8891 (tppt)
REVERT: C  149 ASP cc_start: 0.8559 (t0) cc_final: 0.8315 (t0)
REVERT: C  174 TYR cc_start: 0.7100 (OUTLIER) cc_final: 0.6851 (t80)
REVERT: C  178 PHE cc_start: 0.8943 (m-10) cc_final: 0.8178 (m-10)
REVERT: C  233 ASN cc_start: 0.8799 (m110) cc_final: 0.8450 (p0)
REVERT: C  245 ASP cc_start: 0.9173 (t0) cc_final: 0.8924 (m-30)
REVERT: C  270 ASN cc_start: 0.8810 (m-40) cc_final: 0.8556 (m-40)
REVERT: C  276 TYR cc_start: 0.7894 (t80) cc_final: 0.7673 (t80)
REVERT: C  318 ASP cc_start: 0.9015 (m-30) cc_final: 0.8755 (m-30)
REVERT: D   27 LYS cc_start: 0.8917 (mttt) cc_final: 0.8658 (pttt)
REVERT: D   46 TYR cc_start: 0.8948 (m-10) cc_final: 0.8651 (m-10)
REVERT: D  137 MET cc_start: 0.6028 (mtp) cc_final: 0.5641 (mmt)
REVERT: D  154 PHE cc_start: 0.9307 (t80) cc_final: 0.8856 (t80)
REVERT: D  169 TYR cc_start: 0.8764 (m-80) cc_final: 0.8196 (m-80)
REVERT: D  178 PHE cc_start: 0.9318 (m-80) cc_final: 0.8916 (m-80)
REVERT: D  186 GLN cc_start: 0.8596 (mm110) cc_final: 0.8352 (mp10)
REVERT: D  196 ARG cc_start: 0.8884 (ttp80) cc_final: 0.8625 (ttp80)
REVERT: D  198 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7613 (mm-30)
REVERT: D  213 TYR cc_start: 0.9094 (t80) cc_final: 0.8633 (t80)
REVERT: D  236 TYR cc_start: 0.7963 (t80) cc_final: 0.7615 (t80)
REVERT: D  263 ASN cc_start: 0.8505 (p0) cc_final: 0.8078 (p0)
  outliers start: 50
  outliers final: 34
  residues processed: 573
  average time/residue: 0.1248
  time to fit residues: 106.3899
Evaluate side-chains
  570 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 529
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  227 MET
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  351 SER
Chi-restraints excluded: chain A residue  362 ASP
Chi-restraints excluded: chain A residue  425 ILE
Chi-restraints excluded: chain A residue  435 SER
Chi-restraints excluded: chain A residue  639 ASP
Chi-restraints excluded: chain A residue  684 TYR
Chi-restraints excluded: chain B residue  109 ASN
Chi-restraints excluded: chain B residue  121 ARG
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  410 ASN
Chi-restraints excluded: chain B residue  435 SER
Chi-restraints excluded: chain B residue  441 GLU
Chi-restraints excluded: chain B residue  494 MET
Chi-restraints excluded: chain B residue  584 ILE
Chi-restraints excluded: chain B residue  658 LEU
Chi-restraints excluded: chain B residue  660 ASP
Chi-restraints excluded: chain C residue   21 PHE
Chi-restraints excluded: chain C residue   25 ASN
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain C residue   81 VAL
Chi-restraints excluded: chain C residue  108 ILE
Chi-restraints excluded: chain C residue  174 TYR
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain C residue  196 ARG
Chi-restraints excluded: chain C residue  256 VAL
Chi-restraints excluded: chain D residue   41 LEU
Chi-restraints excluded: chain D residue   76 ILE
Chi-restraints excluded: chain D residue  130 TYR
Chi-restraints excluded: chain D residue  195 LEU
Chi-restraints excluded: chain D residue  200 ILE
Chi-restraints excluded: chain D residue  243 THR
Chi-restraints excluded: chain D residue  250 VAL
Chi-restraints excluded: chain D residue  262 TYR
Chi-restraints excluded: chain D residue  282 ILE
Chi-restraints excluded: chain D residue  315 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 138 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9980
   chunk 28 optimal weight:    3.9990
   chunk 68 optimal weight:    5.9990
   chunk 55 optimal weight:    4.9990
   chunk 184 optimal weight:    9.9990
   chunk 167 optimal weight:    9.9990
   chunk 154 optimal weight:    3.9990
   chunk 174 optimal weight:   10.0000
   chunk 71 optimal weight:    0.8980
   chunk 122 optimal weight:    0.8980
   overall best weight:    2.1584

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

Flipped N/Q/H residues before XYZ refinement:
** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 131 ASN
B 202 ASN
C  24 GLN
** C  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.137251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.095496 restraints weight = 28844.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.098993 restraints weight = 12000.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.101114 restraints weight = 6971.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.102337 restraints weight = 4961.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.103053 restraints weight = 4033.408|
|-----------------------------------------------------------------------------|
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3183
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3183 r_free = 0.3183    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3183 r_free = 0.3183    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3183
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.6058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  16299  Z= 0.216
  Angle     :  0.707  14.729  22004  Z= 0.364
  Chirality :  0.046   0.302   2348
  Planarity :  0.004   0.051   2812
  Dihedral  :  8.550 145.855   2216
  Min Nonbonded Distance : 1.855

Molprobity Statistics.
  All-atom Clashscore : 14.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 26.37 %
    Favored  : 70.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.85 (0.19), residues: 1928
  helix:  1.01 (0.15), residues: 1152
  sheet: -0.55 (0.41), residues: 152
  loop :  0.27 (0.24), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 117 
 TYR   0.023   0.002   TYR C 262 
 PHE   0.050   0.002   PHE D 227 
 TRP   0.032   0.003   TRP D  30 
 HIS   0.017   0.001   HIS C 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00491 (16298)
  covalent geometry    : angle       0.70709 (22004)
  hydrogen bonds       : bond        0.03861 (  896)
  hydrogen bonds       : angle       5.14550 ( 2616)
  Misc. bond           : bond        0.00047 (    1)

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

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

  3856 Ramachandran restraints generated.
    1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3856 Ramachandran restraints generated.
    1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  581 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 529
  time to evaluate  : 0.646 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  228 LYS cc_start: 0.8960 (mtpp) cc_final: 0.8695 (mmtt)
REVERT: A  266 LYS cc_start: 0.8892 (mttp) cc_final: 0.8684 (mttp)
REVERT: A  286 ASP cc_start: 0.8662 (m-30) cc_final: 0.7760 (m-30)
REVERT: A  344 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7662 (mt-10)
REVERT: A  355 TYR cc_start: 0.8953 (m-80) cc_final: 0.8412 (m-80)
REVERT: A  362 ASP cc_start: 0.7763 (OUTLIER) cc_final: 0.6721 (m-30)
REVERT: A  384 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.6387 (pm20)
REVERT: A  485 ARG cc_start: 0.8576 (mtm-85) cc_final: 0.8105 (mtm-85)
REVERT: A  570 MET cc_start: 0.8881 (mtp) cc_final: 0.8552 (mtp)
REVERT: A  639 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.8173 (m-30)
REVERT: A  684 TYR cc_start: 0.8406 (OUTLIER) cc_final: 0.8040 (m-80)
REVERT: B   15 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8144 (mp0)
REVERT: B   98 PHE cc_start: 0.9352 (t80) cc_final: 0.8656 (t80)
REVERT: B  109 ASN cc_start: 0.8876 (OUTLIER) cc_final: 0.8521 (m-40)
REVERT: B  167 LEU cc_start: 0.9155 (mt) cc_final: 0.8637 (mp)
REVERT: B  250 TYR cc_start: 0.9418 (m-80) cc_final: 0.7445 (m-80)
REVERT: B  266 LYS cc_start: 0.8727 (ttmm) cc_final: 0.8436 (ttmm)
REVERT: B  286 ASP cc_start: 0.8094 (m-30) cc_final: 0.7311 (m-30)
REVERT: B  317 MET cc_start: 0.8496 (mtp) cc_final: 0.7992 (mtp)
REVERT: B  342 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9386 (tt)
REVERT: B  355 TYR cc_start: 0.8718 (m-80) cc_final: 0.8468 (m-80)
REVERT: B  357 TYR cc_start: 0.9094 (m-10) cc_final: 0.8730 (m-80)
REVERT: B  362 ASP cc_start: 0.8014 (m-30) cc_final: 0.6537 (m-30)
REVERT: B  379 SER cc_start: 0.9061 (t) cc_final: 0.8284 (t)
REVERT: B  529 ASP cc_start: 0.8172 (m-30) cc_final: 0.7893 (m-30)
REVERT: B  586 TYR cc_start: 0.9163 (m-80) cc_final: 0.8566 (m-80)
REVERT: B  603 GLU cc_start: 0.8333 (tp30) cc_final: 0.8064 (tp30)
REVERT: B  610 LYS cc_start: 0.8511 (tppt) cc_final: 0.8109 (tppt)
REVERT: B  612 TYR cc_start: 0.8533 (m-80) cc_final: 0.7811 (m-80)
REVERT: B  628 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8032 (mt-10)
REVERT: B  668 ASN cc_start: 0.8649 (m-40) cc_final: 0.8295 (m110)
REVERT: C   21 PHE cc_start: 0.8852 (OUTLIER) cc_final: 0.8300 (t80)
REVERT: C   40 ASP cc_start: 0.8925 (p0) cc_final: 0.7990 (p0)
REVERT: C  105 TYR cc_start: 0.8158 (m-80) cc_final: 0.7773 (m-80)
REVERT: C  122 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.7996 (m-10)
REVERT: C  134 LYS cc_start: 0.9247 (pttt) cc_final: 0.8851 (tppt)
REVERT: C  149 ASP cc_start: 0.8521 (t0) cc_final: 0.8252 (t0)
REVERT: C  178 PHE cc_start: 0.9095 (m-10) cc_final: 0.8523 (m-10)
REVERT: C  233 ASN cc_start: 0.8845 (m110) cc_final: 0.8419 (p0)
REVERT: C  242 TYR cc_start: 0.9167 (t80) cc_final: 0.8703 (t80)
REVERT: C  270 ASN cc_start: 0.8831 (m-40) cc_final: 0.8585 (m-40)
REVERT: C  276 TYR cc_start: 0.8066 (t80) cc_final: 0.7806 (t80)
REVERT: C  318 ASP cc_start: 0.9018 (m-30) cc_final: 0.8770 (m-30)
REVERT: D   46 TYR cc_start: 0.8950 (m-10) cc_final: 0.8646 (m-10)
REVERT: D  137 MET cc_start: 0.6282 (mtp) cc_final: 0.5851 (mmp)
REVERT: D  154 PHE cc_start: 0.9329 (t80) cc_final: 0.8916 (t80)
REVERT: D  169 TYR cc_start: 0.8834 (m-80) cc_final: 0.8152 (m-80)
REVERT: D  178 PHE cc_start: 0.9346 (m-80) cc_final: 0.9000 (m-80)
REVERT: D  186 GLN cc_start: 0.8727 (mm110) cc_final: 0.8365 (mp10)
REVERT: D  196 ARG cc_start: 0.8952 (ttp80) cc_final: 0.8665 (ttp80)
REVERT: D  213 TYR cc_start: 0.9026 (t80) cc_final: 0.8642 (t80)
REVERT: D  236 TYR cc_start: 0.7836 (t80) cc_final: 0.7531 (t80)
  outliers start: 52
  outliers final: 35
  residues processed: 549
  average time/residue: 0.1335
  time to fit residues: 109.1788
Evaluate side-chains
  560 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 517
  time to evaluate  : 0.635 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  267 ILE
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  351 SER
Chi-restraints excluded: chain A residue  362 ASP
Chi-restraints excluded: chain A residue  384 GLU
Chi-restraints excluded: chain A residue  425 ILE
Chi-restraints excluded: chain A residue  435 SER
Chi-restraints excluded: chain A residue  639 ASP
Chi-restraints excluded: chain A residue  658 LEU
Chi-restraints excluded: chain A residue  684 TYR
Chi-restraints excluded: chain B residue  109 ASN
Chi-restraints excluded: chain B residue  131 ASN
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  410 ASN
Chi-restraints excluded: chain B residue  435 SER
Chi-restraints excluded: chain B residue  441 GLU
Chi-restraints excluded: chain B residue  494 MET
Chi-restraints excluded: chain B residue  584 ILE
Chi-restraints excluded: chain B residue  658 LEU
Chi-restraints excluded: chain B residue  660 ASP
Chi-restraints excluded: chain B residue  687 THR
Chi-restraints excluded: chain C residue   21 PHE
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain C residue   81 VAL
Chi-restraints excluded: chain C residue  108 ILE
Chi-restraints excluded: chain C residue  122 PHE
Chi-restraints excluded: chain C residue  196 ARG
Chi-restraints excluded: chain D residue   41 LEU
Chi-restraints excluded: chain D residue  106 SER
Chi-restraints excluded: chain D residue  130 TYR
Chi-restraints excluded: chain D residue  189 GLU
Chi-restraints excluded: chain D residue  195 LEU
Chi-restraints excluded: chain D residue  200 ILE
Chi-restraints excluded: chain D residue  250 VAL
Chi-restraints excluded: chain D residue  262 TYR
Chi-restraints excluded: chain D residue  282 ILE
Chi-restraints excluded: chain D residue  315 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 63 optimal weight:    3.9990
   chunk 143 optimal weight:    6.9990
   chunk 28 optimal weight:    0.5980
   chunk 113 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 50 optimal weight:    0.0970
   chunk 107 optimal weight:    5.9990
   chunk 76 optimal weight:    0.6980
   chunk 68 optimal weight:    6.9990
   chunk 12 optimal weight:    0.7980
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
A 150 GLN
** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 668 ASN
B 131 ASN
B 202 ASN
C  25 ASN
** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.142833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.102031 restraints weight = 28587.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.105577 restraints weight = 11799.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.107695 restraints weight = 6708.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.108990 restraints weight = 4741.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.109647 restraints weight = 3842.434|
|-----------------------------------------------------------------------------|
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3260
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3260 r_free = 0.3260    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3260 r_free = 0.3260    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3260
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.6227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  16299  Z= 0.137
  Angle     :  0.704  14.494  22004  Z= 0.358
  Chirality :  0.045   0.318   2348
  Planarity :  0.003   0.050   2812
  Dihedral  :  8.240 137.476   2216
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 13.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 27.71 %
    Favored  : 69.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.96 (0.19), residues: 1928
  helix:  1.07 (0.15), residues: 1155
  sheet:  0.21 (0.45), residues: 126
  loop :  0.13 (0.24), residues: 647

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 686 
 TYR   0.037   0.001   TYR C 247 
 PHE   0.049   0.002   PHE D 227 
 TRP   0.029   0.002   TRP D  30 
 HIS   0.033   0.001   HIS C 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (16298)
  covalent geometry    : angle       0.70422 (22004)
  hydrogen bonds       : bond        0.03678 (  896)
  hydrogen bonds       : angle       5.10536 ( 2616)
  Misc. bond           : bond        0.00019 (    1)

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

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

  3856 Ramachandran restraints generated.
    1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3856 Ramachandran restraints generated.
    1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  595 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 551
  time to evaluate  : 0.636 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ASN cc_start: 0.8896 (m-40) cc_final: 0.8390 (t0)
REVERT: A  218 ASN cc_start: 0.8713 (t0) cc_final: 0.8483 (t0)
REVERT: A  228 LYS cc_start: 0.8958 (mtpp) cc_final: 0.8704 (mmtt)
REVERT: A  250 TYR cc_start: 0.8946 (m-80) cc_final: 0.7616 (m-80)
REVERT: A  266 LYS cc_start: 0.8916 (mttp) cc_final: 0.8683 (mttp)
REVERT: A  286 ASP cc_start: 0.8642 (m-30) cc_final: 0.7931 (m-30)
REVERT: A  344 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7696 (mt-10)
REVERT: A  355 TYR cc_start: 0.8844 (m-80) cc_final: 0.8473 (m-80)
REVERT: A  362 ASP cc_start: 0.7676 (OUTLIER) cc_final: 0.6687 (m-30)
REVERT: A  485 ARG cc_start: 0.8495 (mtm-85) cc_final: 0.7927 (mtm-85)
REVERT: A  570 MET cc_start: 0.8817 (mtp) cc_final: 0.8533 (mtp)
REVERT: A  639 ASP cc_start: 0.8482 (OUTLIER) cc_final: 0.8116 (m-30)
REVERT: A  640 MET cc_start: 0.9227 (tpp) cc_final: 0.7865 (tpp)
REVERT: A  683 TYR cc_start: 0.8862 (t80) cc_final: 0.8558 (t80)
REVERT: A  684 TYR cc_start: 0.8308 (OUTLIER) cc_final: 0.7870 (m-80)
REVERT: B   98 PHE cc_start: 0.9268 (t80) cc_final: 0.8579 (t80)
REVERT: B  109 ASN cc_start: 0.8904 (OUTLIER) cc_final: 0.8567 (m-40)
REVERT: B  121 ARG cc_start: 0.9258 (OUTLIER) cc_final: 0.8794 (tpt170)
REVERT: B  167 LEU cc_start: 0.9081 (mt) cc_final: 0.8551 (mp)
REVERT: B  250 TYR cc_start: 0.9356 (m-80) cc_final: 0.7439 (m-80)
REVERT: B  263 ASP cc_start: 0.8767 (m-30) cc_final: 0.8357 (m-30)
REVERT: B  286 ASP cc_start: 0.8035 (m-30) cc_final: 0.7328 (m-30)
REVERT: B  317 MET cc_start: 0.8385 (mtp) cc_final: 0.7953 (mtp)
REVERT: B  357 TYR cc_start: 0.8955 (m-10) cc_final: 0.8660 (m-80)
REVERT: B  362 ASP cc_start: 0.7995 (m-30) cc_final: 0.6633 (m-30)
REVERT: B  379 SER cc_start: 0.9094 (t) cc_final: 0.8177 (t)
REVERT: B  529 ASP cc_start: 0.7985 (m-30) cc_final: 0.7750 (m-30)
REVERT: B  586 TYR cc_start: 0.9082 (m-80) cc_final: 0.8508 (m-80)
REVERT: B  603 GLU cc_start: 0.8343 (tp30) cc_final: 0.8076 (tp30)
REVERT: B  610 LYS cc_start: 0.8568 (tppt) cc_final: 0.7998 (tppt)
REVERT: B  612 TYR cc_start: 0.8441 (m-80) cc_final: 0.7834 (m-80)
REVERT: B  628 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8157 (mm-30)
REVERT: B  655 THR cc_start: 0.9413 (m) cc_final: 0.9061 (p)
REVERT: C   25 ASN cc_start: 0.8940 (OUTLIER) cc_final: 0.8672 (p0)
REVERT: C   43 THR cc_start: 0.7567 (p) cc_final: 0.7347 (p)
REVERT: C   49 LYS cc_start: 0.8637 (mmmt) cc_final: 0.8342 (ttpp)
REVERT: C  105 TYR cc_start: 0.8270 (m-80) cc_final: 0.8014 (m-80)
REVERT: C  122 PHE cc_start: 0.8447 (OUTLIER) cc_final: 0.8077 (m-10)
REVERT: C  134 LYS cc_start: 0.9194 (pttt) cc_final: 0.8839 (tppt)
REVERT: C  149 ASP cc_start: 0.8679 (t0) cc_final: 0.8441 (t0)
REVERT: C  178 PHE cc_start: 0.8915 (m-10) cc_final: 0.8020 (m-10)
REVERT: C  183 LYS cc_start: 0.7795 (pttm) cc_final: 0.6018 (ttmt)
REVERT: C  233 ASN cc_start: 0.8814 (m110) cc_final: 0.8391 (p0)
REVERT: C  242 TYR cc_start: 0.9173 (t80) cc_final: 0.8847 (t80)
REVERT: C  270 ASN cc_start: 0.8805 (m-40) cc_final: 0.8573 (m-40)
REVERT: C  276 TYR cc_start: 0.7999 (t80) cc_final: 0.7794 (t80)
REVERT: C  318 ASP cc_start: 0.8995 (m-30) cc_final: 0.8736 (m-30)
REVERT: D   46 TYR cc_start: 0.8910 (m-10) cc_final: 0.8627 (m-10)
REVERT: D  137 MET cc_start: 0.6367 (mtp) cc_final: 0.5923 (mmt)
REVERT: D  154 PHE cc_start: 0.9329 (t80) cc_final: 0.8942 (t80)
REVERT: D  178 PHE cc_start: 0.9363 (m-80) cc_final: 0.9076 (m-80)
REVERT: D  186 GLN cc_start: 0.8577 (mm110) cc_final: 0.8292 (mp10)
REVERT: D  196 ARG cc_start: 0.8961 (ttp80) cc_final: 0.8710 (ttp80)
REVERT: D  213 TYR cc_start: 0.9056 (t80) cc_final: 0.8709 (t80)
REVERT: D  236 TYR cc_start: 0.7726 (t80) cc_final: 0.7436 (t80)
  outliers start: 44
  outliers final: 30
  residues processed: 572
  average time/residue: 0.1298
  time to fit residues: 111.0960
Evaluate side-chains
  563 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 526
  time to evaluate  : 0.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  351 SER
Chi-restraints excluded: chain A residue  362 ASP
Chi-restraints excluded: chain A residue  425 ILE
Chi-restraints excluded: chain A residue  435 SER
Chi-restraints excluded: chain A residue  639 ASP
Chi-restraints excluded: chain A residue  658 LEU
Chi-restraints excluded: chain A residue  684 TYR
Chi-restraints excluded: chain B residue  109 ASN
Chi-restraints excluded: chain B residue  121 ARG
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  435 SER
Chi-restraints excluded: chain B residue  441 GLU
Chi-restraints excluded: chain B residue  584 ILE
Chi-restraints excluded: chain B residue  658 LEU
Chi-restraints excluded: chain B residue  660 ASP
Chi-restraints excluded: chain B residue  687 THR
Chi-restraints excluded: chain C residue   25 ASN
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain C residue   81 VAL
Chi-restraints excluded: chain C residue  108 ILE
Chi-restraints excluded: chain C residue  122 PHE
Chi-restraints excluded: chain C residue  196 ARG
Chi-restraints excluded: chain C residue  256 VAL
Chi-restraints excluded: chain D residue   41 LEU
Chi-restraints excluded: chain D residue   76 ILE
Chi-restraints excluded: chain D residue  106 SER
Chi-restraints excluded: chain D residue  130 TYR
Chi-restraints excluded: chain D residue  200 ILE
Chi-restraints excluded: chain D residue  211 GLU
Chi-restraints excluded: chain D residue  250 VAL
Chi-restraints excluded: chain D residue  262 TYR
Chi-restraints excluded: chain D residue  315 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 51 optimal weight:    0.9990
   chunk 130 optimal weight:    5.9990
   chunk 191 optimal weight:    0.0020
   chunk 49 optimal weight:    3.9990
   chunk 64 optimal weight:    0.8980
   chunk 12 optimal weight:    0.6980
   chunk 174 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9980
   chunk 121 optimal weight:    0.0870
   chunk 62 optimal weight:    3.9990
   chunk 68 optimal weight:    7.9990
   overall best weight:    0.5366

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

Flipped N/Q/H residues before XYZ refinement:
** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  62 GLN
B 131 ASN
B 180 ASN
B 668 ASN
** C  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 192 ASN
** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.143110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.102124 restraints weight = 28687.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.105663 restraints weight = 12072.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.107802 restraints weight = 6917.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.109065 restraints weight = 4887.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.109735 restraints weight = 3969.028|
|-----------------------------------------------------------------------------|
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3266
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3266 r_free = 0.3266    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3266 r_free = 0.3266    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3266
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.6363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  16299  Z= 0.135
  Angle     :  0.723  13.509  22004  Z= 0.364
  Chirality :  0.045   0.303   2348
  Planarity :  0.004   0.050   2812
  Dihedral  :  8.160 137.509   2216
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 13.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 28.59 %
    Favored  : 69.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.97 (0.19), residues: 1928
  helix:  1.11 (0.15), residues: 1153
  sheet:  0.15 (0.45), residues: 128
  loop :  0.09 (0.24), residues: 647

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 225 
 TYR   0.029   0.001   TYR C 262 
 PHE   0.052   0.002   PHE D 227 
 TRP   0.033   0.002   TRP C  44 
 HIS   0.033   0.001   HIS C 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 (16298)
  covalent geometry    : angle       0.72315 (22004)
  hydrogen bonds       : bond        0.03674 (  896)
  hydrogen bonds       : angle       5.08236 ( 2616)
  Misc. bond           : bond        0.00018 (    1)

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

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

  3856 Ramachandran restraints generated.
    1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3856 Ramachandran restraints generated.
    1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  574 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 537
  time to evaluate  : 0.713 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ASN cc_start: 0.8861 (m-40) cc_final: 0.8342 (t0)
REVERT: A  218 ASN cc_start: 0.8680 (t0) cc_final: 0.8454 (t0)
REVERT: A  228 LYS cc_start: 0.8953 (mtpp) cc_final: 0.8696 (mmtt)
REVERT: A  250 TYR cc_start: 0.8922 (m-80) cc_final: 0.7634 (m-80)
REVERT: A  266 LYS cc_start: 0.8898 (mttp) cc_final: 0.8642 (mttp)
REVERT: A  286 ASP cc_start: 0.8718 (m-30) cc_final: 0.8258 (m-30)
REVERT: A  344 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7654 (mt-10)
REVERT: A  355 TYR cc_start: 0.8833 (m-80) cc_final: 0.8486 (m-80)
REVERT: A  362 ASP cc_start: 0.7664 (OUTLIER) cc_final: 0.6693 (m-30)
REVERT: A  384 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.6162 (pm20)
REVERT: A  485 ARG cc_start: 0.8495 (mtm-85) cc_final: 0.7639 (mtm110)
REVERT: A  570 MET cc_start: 0.8754 (mtp) cc_final: 0.8452 (mtp)
REVERT: A  602 GLU cc_start: 0.7676 (tm-30) cc_final: 0.6270 (tm-30)
REVERT: A  639 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.8094 (m-30)
REVERT: A  640 MET cc_start: 0.9178 (tpp) cc_final: 0.7797 (tpp)
REVERT: A  683 TYR cc_start: 0.8849 (t80) cc_final: 0.8436 (t80)
REVERT: A  684 TYR cc_start: 0.8258 (OUTLIER) cc_final: 0.7793 (m-80)
REVERT: B   98 PHE cc_start: 0.9282 (t80) cc_final: 0.8554 (t80)
REVERT: B  109 ASN cc_start: 0.8828 (OUTLIER) cc_final: 0.8511 (m-40)
REVERT: B  121 ARG cc_start: 0.9283 (OUTLIER) cc_final: 0.8782 (tpt170)
REVERT: B  250 TYR cc_start: 0.9343 (m-80) cc_final: 0.7529 (m-80)
REVERT: B  263 ASP cc_start: 0.8751 (m-30) cc_final: 0.8267 (m-30)
REVERT: B  286 ASP cc_start: 0.8009 (m-30) cc_final: 0.7301 (m-30)
REVERT: B  362 ASP cc_start: 0.7947 (m-30) cc_final: 0.6603 (m-30)
REVERT: B  374 SER cc_start: 0.9314 (t) cc_final: 0.9012 (m)
REVERT: B  379 SER cc_start: 0.9087 (t) cc_final: 0.8277 (t)
REVERT: B  529 ASP cc_start: 0.7987 (m-30) cc_final: 0.7778 (m-30)
REVERT: B  586 TYR cc_start: 0.9022 (m-80) cc_final: 0.8514 (m-80)
REVERT: B  610 LYS cc_start: 0.8565 (tppt) cc_final: 0.8184 (tppt)
REVERT: B  612 TYR cc_start: 0.8351 (m-80) cc_final: 0.7630 (m-80)
REVERT: B  615 MET cc_start: 0.9082 (mmm) cc_final: 0.8872 (mmp)
REVERT: B  655 THR cc_start: 0.9432 (m) cc_final: 0.9126 (p)
REVERT: B  668 ASN cc_start: 0.8431 (m-40) cc_final: 0.8155 (m110)
REVERT: C   82 ASP cc_start: 0.8436 (m-30) cc_final: 0.8003 (p0)
REVERT: C   91 ASN cc_start: 0.9426 (m-40) cc_final: 0.9208 (m-40)
REVERT: C  105 TYR cc_start: 0.8371 (m-80) cc_final: 0.8133 (m-80)
REVERT: C  107 ASN cc_start: 0.8885 (p0) cc_final: 0.8603 (p0)
REVERT: C  129 LYS cc_start: 0.9102 (ptpp) cc_final: 0.8890 (tmmt)
REVERT: C  134 LYS cc_start: 0.9168 (pttt) cc_final: 0.8792 (tppt)
REVERT: C  137 MET cc_start: 0.8400 (ptp) cc_final: 0.8011 (ptt)
REVERT: C  178 PHE cc_start: 0.8899 (m-10) cc_final: 0.8572 (m-10)
REVERT: C  233 ASN cc_start: 0.8831 (m110) cc_final: 0.8432 (p0)
REVERT: C  242 TYR cc_start: 0.9187 (t80) cc_final: 0.8829 (t80)
REVERT: C  270 ASN cc_start: 0.8800 (m-40) cc_final: 0.8574 (m-40)
REVERT: C  276 TYR cc_start: 0.8112 (t80) cc_final: 0.7862 (t80)
REVERT: D   46 TYR cc_start: 0.8912 (m-10) cc_final: 0.8661 (m-10)
REVERT: D   74 MET cc_start: 0.7276 (tpp) cc_final: 0.5847 (ttm)
REVERT: D  137 MET cc_start: 0.6458 (mtp) cc_final: 0.5994 (mmt)
REVERT: D  154 PHE cc_start: 0.9351 (t80) cc_final: 0.8961 (t80)
REVERT: D  178 PHE cc_start: 0.9362 (m-80) cc_final: 0.8951 (m-80)
REVERT: D  186 GLN cc_start: 0.8570 (mm110) cc_final: 0.8332 (mp10)
REVERT: D  196 ARG cc_start: 0.8984 (ttp80) cc_final: 0.8722 (ttp80)
REVERT: D  213 TYR cc_start: 0.9053 (t80) cc_final: 0.8706 (t80)
REVERT: D  236 TYR cc_start: 0.7755 (t80) cc_final: 0.7486 (t80)
  outliers start: 37
  outliers final: 26
  residues processed: 553
  average time/residue: 0.1316
  time to fit residues: 109.0856
Evaluate side-chains
  550 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 518
  time to evaluate  : 0.622 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  213 ILE
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  351 SER
Chi-restraints excluded: chain A residue  362 ASP
Chi-restraints excluded: chain A residue  384 GLU
Chi-restraints excluded: chain A residue  425 ILE
Chi-restraints excluded: chain A residue  435 SER
Chi-restraints excluded: chain A residue  639 ASP
Chi-restraints excluded: chain A residue  658 LEU
Chi-restraints excluded: chain A residue  684 TYR
Chi-restraints excluded: chain B residue  109 ASN
Chi-restraints excluded: chain B residue  121 ARG
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  435 SER
Chi-restraints excluded: chain B residue  441 GLU
Chi-restraints excluded: chain B residue  584 ILE
Chi-restraints excluded: chain B residue  658 LEU
Chi-restraints excluded: chain B residue  660 ASP
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain C residue   81 VAL
Chi-restraints excluded: chain C residue  108 ILE
Chi-restraints excluded: chain C residue  196 ARG
Chi-restraints excluded: chain C residue  256 VAL
Chi-restraints excluded: chain D residue   41 LEU
Chi-restraints excluded: chain D residue   76 ILE
Chi-restraints excluded: chain D residue  130 TYR
Chi-restraints excluded: chain D residue  200 ILE
Chi-restraints excluded: chain D residue  262 TYR
Chi-restraints excluded: chain D residue  315 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 97 optimal weight:    3.9990
   chunk 123 optimal weight:    3.9990
   chunk 151 optimal weight:    4.9990
   chunk 162 optimal weight:    9.9990
   chunk 146 optimal weight:    0.7980
   chunk 96 optimal weight:    0.4980
   chunk 16 optimal weight:    0.5980
   chunk 147 optimal weight:   10.0000
   chunk 120 optimal weight:    2.9990
   chunk 135 optimal weight:    0.6980
   chunk 80 optimal weight:    2.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 131 ASN
C  25 ASN
** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  71 ASN
** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.141872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.101045 restraints weight = 28641.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.104577 restraints weight = 11862.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.106612 restraints weight = 6804.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.107916 restraints weight = 4871.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.108513 restraints weight = 3940.763|
|-----------------------------------------------------------------------------|
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3241
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3241 r_free = 0.3241    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3241 r_free = 0.3241    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3241
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.6423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  16299  Z= 0.157
  Angle     :  0.731  13.410  22004  Z= 0.372
  Chirality :  0.046   0.295   2348
  Planarity :  0.004   0.049   2812
  Dihedral  :  8.184 140.280   2216
  Min Nonbonded Distance : 1.928

Molprobity Statistics.
  All-atom Clashscore : 14.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 28.76 %
    Favored  : 69.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.92 (0.19), residues: 1928
  helix:  1.05 (0.15), residues: 1156
  sheet:  0.18 (0.46), residues: 128
  loop :  0.09 (0.24), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 225 
 TYR   0.044   0.001   TYR C 247 
 PHE   0.052   0.002   PHE D 227 
 TRP   0.046   0.003   TRP C  44 
 HIS   0.033   0.001   HIS C 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 (16298)
  covalent geometry    : angle       0.73139 (22004)
  hydrogen bonds       : bond        0.03745 (  896)
  hydrogen bonds       : angle       5.12727 ( 2616)
  Misc. bond           : bond        0.00027 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3569.04 seconds
wall clock time: 62 minutes 26.17 seconds (3746.17 seconds total)