Starting phenix.real_space_refine
on Wed Sep 17 22:21:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9eao_47838/09_2025/9eao_47838.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9eao_47838/09_2025/9eao_47838.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9eao_47838/09_2025/9eao_47838.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9eao_47838/09_2025/9eao_47838.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9eao_47838/09_2025/9eao_47838.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9eao_47838/09_2025/9eao_47838.cif"
  }
  resolution = 2.6
  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=   0.003 sd=   0.475
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: 5
    Type Number    sf(0)   Gaussians
     Ca      3      9.91       5
     S      48      5.16       5
     C    7602      2.51       5
     N    1941      2.21       5
     O    2204      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 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: 11798
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3949
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 514, 3949
          Classifications: {'peptide': 514}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 44, 'TRANS': 467}
    Chain: "B"
      Number of atoms: 3963
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 516, 3963
          Classifications: {'peptide': 516}
          Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 470}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 3883
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 504, 3883
          Classifications: {'peptide': 504}
          Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 459}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.94, per 1000 atoms: 0.25
  Number of scatterers: 11798
  At special positions: 0
  Unit cell: (119.9, 116.6, 123.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      3     19.99
     S      48     16.00
     O    2204      8.00
     N    1941      7.00
     C    7602      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=0, symmetry=0
  Time building additional restraints: 0.84
  Conformation dependent library (CDL) restraints added in 549.3 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  3046 Ramachandran restraints generated.
    1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2842

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 19 sheets defined
      10.6% alpha, 32.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.49
  Creating SS restraints...
    Processing helix  chain 'A' and resid 37 through 42
      removed outlier: 3.500A  pdb=" N   ALA A  41 " --> pdb=" O   GLY A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 43 through 45
      No H-bonds generated for 'chain 'A' and resid 43 through 45'
    Processing helix  chain 'A' and resid 54 through 58
      removed outlier: 4.164A  pdb=" N   ASN A  58 " --> pdb=" O   ILE A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 96
    Processing helix  chain 'A' and resid 97 through 99
      No H-bonds generated for 'chain 'A' and resid 97 through 99'
    Processing helix  chain 'A' and resid 140 through 144
      removed outlier: 3.779A  pdb=" N   PHE A 144 " --> pdb=" O   ILE A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 240
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.569A  pdb=" N   TRP A 285 " --> pdb=" O   SER A 282 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   VAL A 286 " --> pdb=" O   GLY A 283 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 282 through 286'
    Processing helix  chain 'A' and resid 368 through 371
    Processing helix  chain 'B' and resid 37 through 45
      removed outlier: 3.854A  pdb=" N   ALA B  42 " --> pdb=" O   ALA B  39 " (cutoff:3.500A)
      Proline residue:  B  43  - end of helix
    Processing helix  chain 'B' and resid 54 through 58
      removed outlier: 4.102A  pdb=" N   ASN B  58 " --> pdb=" O   ILE B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 85 through 88
      removed outlier: 3.657A  pdb=" N   LEU B  88 " --> pdb=" O   GLY B  85 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 85 through 88'
    Processing helix  chain 'B' and resid 89 through 96
    Processing helix  chain 'B' and resid 97 through 99
      No H-bonds generated for 'chain 'B' and resid 97 through 99'
    Processing helix  chain 'B' and resid 140 through 144
      removed outlier: 3.818A  pdb=" N   PHE B 144 " --> pdb=" O   ILE B 141 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 236 through 240
    Processing helix  chain 'B' and resid 282 through 286
      removed outlier: 3.615A  pdb=" N   TRP B 285 " --> pdb=" O   SER B 282 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   VAL B 286 " --> pdb=" O   GLY B 283 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 282 through 286'
    Processing helix  chain 'B' and resid 368 through 371
    Processing helix  chain 'B' and resid 454 through 465
    Processing helix  chain 'C' and resid 37 through 42
      removed outlier: 3.543A  pdb=" N   ALA C  41 " --> pdb=" O   GLY C  37 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 43 through 45
      No H-bonds generated for 'chain 'C' and resid 43 through 45'
    Processing helix  chain 'C' and resid 52 through 58
      removed outlier: 3.784A  pdb=" N   ASN C  58 " --> pdb=" O   ILE C  55 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 85 through 88
    Processing helix  chain 'C' and resid 89 through 96
    Processing helix  chain 'C' and resid 97 through 99
      No H-bonds generated for 'chain 'C' and resid 97 through 99'
    Processing helix  chain 'C' and resid 139 through 144
      removed outlier: 3.775A  pdb=" N   THR C 142 " --> pdb=" O   ALA C 139 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   PHE C 144 " --> pdb=" O   ILE C 141 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 236 through 240
    Processing helix  chain 'C' and resid 282 through 286
      removed outlier: 3.782A  pdb=" N   VAL C 286 " --> pdb=" O   GLY C 283 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 454 through 465
    Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 69
      removed outlier: 12.617A  pdb=" N   GLN A  61 " --> pdb=" O   PRO A 209 " (cutoff:3.500A)
      removed outlier: 10.907A  pdb=" N   SER A 207 " --> pdb=" O   PRO A  63 " (cutoff:3.500A)
      removed outlier: 5.248A  pdb=" N   GLY A  65 " --> pdb=" O   LEU A 205 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   LEU A 205 " --> pdb=" O   GLY A  65 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   SER A 202 " --> pdb=" O   ALA A 113 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 83
      removed outlier: 6.766A  pdb=" N   CYS A 183 " --> pdb=" O   LEU A  79 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   ASP A  81 " --> pdb=" O   LEU A 181 " (cutoff:3.500A)
      removed outlier: 6.207A  pdb=" N   LEU A 181 " --> pdb=" O   ASP A  81 " (cutoff:3.500A)
      removed outlier: 7.126A  pdb=" N   VAL A 182 " --> pdb=" O   VAL A 127 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   VAL A 127 " --> pdb=" O   VAL A 182 " (cutoff:3.500A)
      removed outlier: 7.976A  pdb=" N   MET A 184 " --> pdb=" O   ALA A 125 " (cutoff:3.500A)
      removed outlier: 7.722A  pdb=" N   ALA A 125 " --> pdb=" O   MET A 184 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   TYR A 186 " --> pdb=" O   VAL A 123 " (cutoff:3.500A)
      removed outlier: 7.426A  pdb=" N   VAL A 123 " --> pdb=" O   TYR A 186 " (cutoff:3.500A)
      removed outlier: 5.236A  pdb=" N   LYS A 121 " --> pdb=" O   PRO A 188 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 171
    Processing sheet with id=AA4, first strand: chain 'A' and resid 448 through 451
    Processing sheet with id=AA5, first strand: chain 'A' and resid 448 through 451
      removed outlier: 5.372A  pdb=" N   ILE A 497 " --> pdb=" O   LEU A 430 " (cutoff:3.500A)
      removed outlier: 5.234A  pdb=" N   SER A 500 " --> pdb=" O   GLU A 488 " (cutoff:3.500A)
      removed outlier: 8.117A  pdb=" N   GLU A 488 " --> pdb=" O   SER A 500 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   LEU A 485 " --> pdb=" O   ASN A 479 " (cutoff:3.500A)
      removed outlier: 6.840A  pdb=" N   ASN A 479 " --> pdb=" O   LEU A 485 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   PHE A 487 " --> pdb=" O   TYR A 477 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   ALA A 472 " --> pdb=" O   TRP A 520 " (cutoff:3.500A)
      removed outlier: 4.595A  pdb=" N   TRP A 520 " --> pdb=" O   ALA A 472 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   LEU A 474 " --> pdb=" O   VAL A 518 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 289 through 297
      removed outlier: 4.294A  pdb=" N   ALA A 290 " --> pdb=" O   ILE A 310 " (cutoff:3.500A)
      removed outlier: 6.948A  pdb=" N   PHE A 375 " --> pdb=" O   ILE A 358 " (cutoff:3.500A)
      removed outlier: 4.947A  pdb=" N   ILE A 358 " --> pdb=" O   PHE A 375 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   SER A 332 " --> pdb=" O   PHE A 401 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   PHE A 401 " --> pdb=" O   SER A 332 " (cutoff:3.500A)
      removed outlier: 6.084A  pdb=" N   GLU A 338 " --> pdb=" O   PRO A 395 " (cutoff:3.500A)
      removed outlier: 9.197A  pdb=" N   GLN A 340 " --> pdb=" O   ALA A 393 " (cutoff:3.500A)
      removed outlier: 8.550A  pdb=" N   ALA A 393 " --> pdb=" O   GLN A 340 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   GLY A 389 " --> pdb=" O   ALA A 293 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 60 through 69
      removed outlier: 12.790A  pdb=" N   GLN B  61 " --> pdb=" O   PRO B 209 " (cutoff:3.500A)
      removed outlier: 11.130A  pdb=" N   SER B 207 " --> pdb=" O   PRO B  63 " (cutoff:3.500A)
      removed outlier: 4.999A  pdb=" N   GLY B  65 " --> pdb=" O   LEU B 205 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 78 through 83
      removed outlier: 6.809A  pdb=" N   ILE B  78 " --> pdb=" O   LEU B 185 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   LEU B 185 " --> pdb=" O   ILE B  78 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   PHE B  80 " --> pdb=" O   CYS B 183 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   LYS B 121 " --> pdb=" O   TYR B 186 " (cutoff:3.500A)
      removed outlier: 6.118A  pdb=" N   ALA B 119 " --> pdb=" O   PRO B 188 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 102 through 103
    Processing sheet with id=AB1, first strand: chain 'B' and resid 447 through 451
      removed outlier: 4.772A  pdb=" N   GLU B 447 " --> pdb=" O   MET B 436 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   LEU B 252 " --> pdb=" O   PHE B 509 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 447 through 451
      removed outlier: 4.772A  pdb=" N   GLU B 447 " --> pdb=" O   MET B 436 " (cutoff:3.500A)
      removed outlier: 5.605A  pdb=" N   ILE B 497 " --> pdb=" O   LEU B 430 " (cutoff:3.500A)
      removed outlier: 5.350A  pdb=" N   SER B 500 " --> pdb=" O   GLU B 488 " (cutoff:3.500A)
      removed outlier: 8.022A  pdb=" N   GLU B 488 " --> pdb=" O   SER B 500 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   TYR B 477 " --> pdb=" O   LEU B 486 " (cutoff:3.500A)
      removed outlier: 4.527A  pdb=" N   GLU B 488 " --> pdb=" O   LEU B 475 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   LEU B 475 " --> pdb=" O   GLU B 488 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   LYS B 490 " --> pdb=" O   LEU B 473 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   LEU B 473 " --> pdb=" O   LYS B 490 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   ALA B 472 " --> pdb=" O   TRP B 520 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   TRP B 520 " --> pdb=" O   ALA B 472 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   LEU B 474 " --> pdb=" O   VAL B 518 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 289 through 298
      removed outlier: 4.170A  pdb=" N   ALA B 290 " --> pdb=" O   ILE B 310 " (cutoff:3.500A)
      removed outlier: 7.333A  pdb=" N   PHE B 375 " --> pdb=" O   ILE B 358 " (cutoff:3.500A)
      removed outlier: 5.439A  pdb=" N   ILE B 358 " --> pdb=" O   PHE B 375 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   SER B 332 " --> pdb=" O   PHE B 401 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   PHE B 401 " --> pdb=" O   SER B 332 " (cutoff:3.500A)
      removed outlier: 5.890A  pdb=" N   GLU B 338 " --> pdb=" O   PRO B 395 " (cutoff:3.500A)
      removed outlier: 9.109A  pdb=" N   GLN B 340 " --> pdb=" O   ALA B 393 " (cutoff:3.500A)
      removed outlier: 8.355A  pdb=" N   ALA B 393 " --> pdb=" O   GLN B 340 " (cutoff:3.500A)
      removed outlier: 11.866A  pdb=" N   GLU B 342 " --> pdb=" O   VAL B 391 " (cutoff:3.500A)
      removed outlier: 11.519A  pdb=" N   VAL B 391 " --> pdb=" O   GLU B 342 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 60 through 69
      removed outlier: 12.605A  pdb=" N   GLN C  61 " --> pdb=" O   PRO C 209 " (cutoff:3.500A)
      removed outlier: 9.682A  pdb=" N   SER C 207 " --> pdb=" O   PRO C  63 " (cutoff:3.500A)
      removed outlier: 5.687A  pdb=" N   GLY C  65 " --> pdb=" O   LEU C 205 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   SER C 202 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 78 through 83
      removed outlier: 6.828A  pdb=" N   ILE C  78 " --> pdb=" O   LEU C 185 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   LEU C 185 " --> pdb=" O   ILE C  78 " (cutoff:3.500A)
      removed outlier: 6.205A  pdb=" N   LYS C 121 " --> pdb=" O   TYR C 186 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 170 through 171
    Processing sheet with id=AB7, first strand: chain 'C' and resid 449 through 451
      removed outlier: 3.547A  pdb=" N   GLY C 251 " --> pdb=" O   ARG C 433 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   LEU C 252 " --> pdb=" O   PHE C 509 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'C' and resid 350 through 354
      removed outlier: 3.639A  pdb=" N   THR C 353 " --> pdb=" O   ILE C 339 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ILE C 339 " --> pdb=" O   THR C 353 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 350 through 354
      removed outlier: 3.639A  pdb=" N   THR C 353 " --> pdb=" O   ILE C 339 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ILE C 339 " --> pdb=" O   THR C 353 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   SER C 332 " --> pdb=" O   PHE C 401 " (cutoff:3.500A)
      removed outlier: 4.529A  pdb=" N   PHE C 401 " --> pdb=" O   SER C 332 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   SER C 397 " --> pdb=" O   GLU C 336 " (cutoff:3.500A)
      removed outlier: 6.037A  pdb=" N   GLU C 338 " --> pdb=" O   PRO C 395 " (cutoff:3.500A)
      removed outlier: 9.169A  pdb=" N   GLN C 340 " --> pdb=" O   ALA C 393 " (cutoff:3.500A)
      removed outlier: 8.758A  pdb=" N   ALA C 393 " --> pdb=" O   GLN C 340 " (cutoff:3.500A)
      removed outlier: 11.781A  pdb=" N   GLU C 342 " --> pdb=" O   VAL C 391 " (cutoff:3.500A)
      removed outlier: 11.430A  pdb=" N   VAL C 391 " --> pdb=" O   GLU C 342 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   ALA C 290 " --> pdb=" O   ILE C 310 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'C' and resid 427 through 429
      removed outlier: 5.245A  pdb=" N   SER C 500 " --> pdb=" O   GLU C 488 " (cutoff:3.500A)
      removed outlier: 8.163A  pdb=" N   GLU C 488 " --> pdb=" O   SER C 500 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   TYR C 477 " --> pdb=" O   LEU C 486 " (cutoff:3.500A)
      removed outlier: 4.799A  pdb=" N   GLU C 488 " --> pdb=" O   LEU C 475 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   LEU C 475 " --> pdb=" O   GLU C 488 " (cutoff:3.500A)
      removed outlier: 4.514A  pdb=" N   LYS C 490 " --> pdb=" O   LEU C 473 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   LEU C 473 " --> pdb=" O   LYS C 490 " (cutoff:3.500A)
      removed outlier: 7.011A  pdb=" N   ALA C 472 " --> pdb=" O   TRP C 520 " (cutoff:3.500A)
      removed outlier: 4.712A  pdb=" N   TRP C 520 " --> pdb=" O   ALA C 472 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   LEU C 474 " --> pdb=" O   VAL C 518 " (cutoff:3.500A)

    316 hydrogen bonds defined for protein.
    786 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: 1.98

  Time building geometry restraints manager: 1.16 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3828
        1.34 -     1.46: 2085
        1.46 -     1.57: 6133
        1.57 -     1.69: 0
        1.69 -     1.81: 72
  Bond restraints: 12118
  Sorted by residual:
  bond pdb=" CB  PRO B  23 "
       pdb=" CG  PRO B  23 "
    ideal  model  delta    sigma   weight residual
    1.492  1.568 -0.076 5.00e-02 4.00e+02 2.33e+00
  bond pdb=" CG  PRO B  23 "
       pdb=" CD  PRO B  23 "
    ideal  model  delta    sigma   weight residual
    1.503  1.545 -0.042 3.40e-02 8.65e+02 1.53e+00
  bond pdb=" CA  ASP B 174 "
       pdb=" CB  ASP B 174 "
    ideal  model  delta    sigma   weight residual
    1.530  1.544 -0.014 1.69e-02 3.50e+03 7.15e-01
  bond pdb=" CB  ILE A 405 "
       pdb=" CG1 ILE A 405 "
    ideal  model  delta    sigma   weight residual
    1.530  1.547 -0.017 2.00e-02 2.50e+03 7.03e-01
  bond pdb=" C   LEU C 159 "
       pdb=" N   PRO C 160 "
    ideal  model  delta    sigma   weight residual
    1.330  1.340 -0.010 1.23e-02 6.61e+03 6.93e-01
  ... (remaining 12113 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.26: 16370
        2.26 -     4.53: 220
        4.53 -     6.79: 13
        6.79 -     9.06: 6
        9.06 -    11.32: 3
  Bond angle restraints: 16612
  Sorted by residual:
  angle pdb=" C   THR C 363 "
        pdb=" CA  THR C 363 "
        pdb=" CB  THR C 363 "
      ideal   model   delta    sigma   weight residual
     116.54  110.04    6.50 1.15e+00 7.56e-01 3.19e+01
  angle pdb=" C   GLN C 469 "
        pdb=" N   SER C 470 "
        pdb=" CA  SER C 470 "
      ideal   model   delta    sigma   weight residual
     121.90  115.00    6.90 1.26e+00 6.30e-01 3.00e+01
  angle pdb=" CA  PRO B  23 "
        pdb=" N   PRO B  23 "
        pdb=" CD  PRO B  23 "
      ideal   model   delta    sigma   weight residual
     112.00  106.63    5.37 1.40e+00 5.10e-01 1.47e+01
  angle pdb=" CA  THR C 363 "
        pdb=" C   THR C 363 "
        pdb=" N   ASN C 364 "
      ideal   model   delta    sigma   weight residual
     119.52  116.53    2.99 7.90e-01 1.60e+00 1.43e+01
  angle pdb=" N   PHE A 423 "
        pdb=" CA  PHE A 423 "
        pdb=" C   PHE A 423 "
      ideal   model   delta    sigma   weight residual
     110.35  115.58   -5.23 1.40e+00 5.10e-01 1.39e+01
  ... (remaining 16607 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.39: 6197
       17.39 -    34.78: 690
       34.78 -    52.17: 222
       52.17 -    69.56: 62
       69.56 -    86.95: 18
  Dihedral angle restraints: 7189
    sinusoidal: 2762
      harmonic: 4427
  Sorted by residual:
  dihedral pdb=" CA  GLY B 195 "
           pdb=" C   GLY B 195 "
           pdb=" N   ASP B 196 "
           pdb=" CA  ASP B 196 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.33   30.67     0      5.00e+00 4.00e-02 3.76e+01
  dihedral pdb=" CA  VAL B  22 "
           pdb=" C   VAL B  22 "
           pdb=" N   PRO B  23 "
           pdb=" CA  PRO B  23 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.02  -26.98     0      5.00e+00 4.00e-02 2.91e+01
  dihedral pdb=" CA  GLY A 421 "
           pdb=" C   GLY A 421 "
           pdb=" N   PRO A 422 "
           pdb=" CA  PRO A 422 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00  -25.80   25.80     0      5.00e+00 4.00e-02 2.66e+01
  ... (remaining 7186 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1393
       0.044 -    0.089: 333
       0.089 -    0.133: 162
       0.133 -    0.178: 3
       0.178 -    0.222: 1
  Chirality restraints: 1892
  Sorted by residual:
  chirality pdb=" CA  PRO B  23 "
            pdb=" N   PRO B  23 "
            pdb=" C   PRO B  23 "
            pdb=" CB  PRO B  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.50    0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" CG  LEU B  64 "
            pdb=" CB  LEU B  64 "
            pdb=" CD1 LEU B  64 "
            pdb=" CD2 LEU B  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.41   -0.18 2.00e-01 2.50e+01 7.75e-01
  chirality pdb=" CA  PRO C 129 "
            pdb=" N   PRO C 129 "
            pdb=" C   PRO C 129 "
            pdb=" CB  PRO C 129 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 5.06e-01
  ... (remaining 1889 not shown)

  Planarity restraints: 2174
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B  22 "   -0.093 5.00e-02 4.00e+02   1.40e-01 3.14e+01
        pdb=" N   PRO B  23 "    0.242 5.00e-02 4.00e+02
        pdb=" CA  PRO B  23 "   -0.076 5.00e-02 4.00e+02
        pdb=" CD  PRO B  23 "   -0.073 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO C 128 "   -0.040 5.00e-02 4.00e+02   6.08e-02 5.91e+00
        pdb=" N   PRO C 129 "    0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO C 129 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO C 129 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS B  62 "    0.038 5.00e-02 4.00e+02   5.80e-02 5.38e+00
        pdb=" N   PRO B  63 "   -0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO B  63 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO B  63 "    0.032 5.00e-02 4.00e+02
  ... (remaining 2171 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 143
        2.66 -     3.22: 9533
        3.22 -     3.78: 16554
        3.78 -     4.34: 23779
        4.34 -     4.90: 40143
  Nonbonded interactions: 90152
  Sorted by model distance:
  nonbonded pdb=" OG  SER C 383 "
            pdb=" OD1 ASP C 385 "
     model   vdw
     2.103 3.040
  nonbonded pdb=" ND2 ASN C 261 "
            pdb=" O   ILE C 420 "
     model   vdw
     2.266 3.120
  nonbonded pdb=" ND1 HIS C 270 "
            pdb=" OD1 ASP C 272 "
     model   vdw
     2.296 3.120
  nonbonded pdb=" ND2 ASN B 261 "
            pdb=" O   ILE B 420 "
     model   vdw
     2.307 3.120
  nonbonded pdb=" ND2 ASN B  49 "
            pdb=" O   VAL B 216 "
     model   vdw
     2.316 3.120
  ... (remaining 90147 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 27 through 530 or resid 601))
  selection = (chain 'B' and resid 27 through 601)
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             9.640
  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:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     11.850
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.010
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.076  12118  Z= 0.123
  Angle     :  0.623  11.321  16612  Z= 0.324
  Chirality :  0.046   0.222   1892
  Planarity :  0.007   0.140   2174
  Dihedral  : 17.272  86.950   4347
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  5.58 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 22.41 %
    Favored  : 72.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -1.14 (0.19), residues: 1523
  helix: -0.25 (0.66), residues: 50
  sheet:  0.06 (0.24), residues: 406
  loop : -1.18 (0.17), residues: 1067

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 165 
 TYR   0.016   0.001   TYR A 217 
 PHE   0.017   0.001   PHE C  80 
 TRP   0.011   0.001   TRP C 169 
 HIS   0.002   0.001   HIS A 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 (12118)
  covalent geometry    : angle       0.62278 (16612)
  hydrogen bonds       : bond        0.17064 (  305)
  hydrogen bonds       : angle       6.60433 (  786)

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

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

  3046 Ramachandran restraints generated.
    1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3046 Ramachandran restraints generated.
    1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 152
  time to evaluate  : 0.492 
Fit side-chains
  outliers start: 66
  outliers final: 64
  residues processed: 214
  average time/residue: 0.5349
  time to fit residues: 124.7538
Evaluate side-chains
  208 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 144
  time to evaluate  : 0.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  214 ASN
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  344 THR
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  377 SER
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  438 GLN
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   28 GLN
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  106 MET
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain B residue  142 THR
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain B residue  193 SER
Chi-restraints excluded: chain B residue  196 ASP
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  337 ILE
Chi-restraints excluded: chain B residue  344 THR
Chi-restraints excluded: chain B residue  378 VAL
Chi-restraints excluded: chain B residue  388 ASP
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  482 THR
Chi-restraints excluded: chain B residue  511 THR
Chi-restraints excluded: chain B residue  529 SER
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   68 SER
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  141 ILE
Chi-restraints excluded: chain C residue  158 GLN
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain C residue  234 VAL
Chi-restraints excluded: chain C residue  257 SER
Chi-restraints excluded: chain C residue  260 SER
Chi-restraints excluded: chain C residue  308 THR
Chi-restraints excluded: chain C residue  346 THR
Chi-restraints excluded: chain C residue  353 THR
Chi-restraints excluded: chain C residue  374 VAL
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  388 ASP
Chi-restraints excluded: chain C residue  434 THR
Chi-restraints excluded: chain C residue  485 LEU
Chi-restraints excluded: chain C residue  499 LEU
Chi-restraints excluded: chain C residue  508 THR
Chi-restraints excluded: chain C residue  511 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 98 optimal weight:   20.0000
   chunk 107 optimal weight:    9.9990
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    8.9990
   chunk 130 optimal weight:   20.0000
   chunk 124 optimal weight:   20.0000
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    3.9990
   chunk 149 optimal weight:    8.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 261 ASN
A 402 GLN
B 334 GLN
B 367 GLN
B 402 GLN
B 438 GLN
C 479 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.179466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.116614 restraints weight = 11828.145|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 1.55
r_work: 0.3215 rms_B_bonded: 1.79 restraints_weight: 0.5000
r_work: 0.3132 rms_B_bonded: 2.94 restraints_weight: 0.2500
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
moved from start:          0.0482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071  12118  Z= 0.164
  Angle     :  0.686  11.774  16612  Z= 0.352
  Chirality :  0.048   0.228   1892
  Planarity :  0.007   0.141   2174
  Dihedral  :  8.978  59.954   1743
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 3.16
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  5.58 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  7.23 %
    Allowed  : 19.58 %
    Favored  : 73.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    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: -1.15 (0.20), residues: 1523
  helix: -0.80 (0.64), residues: 52
  sheet:  0.05 (0.24), residues: 412
  loop : -1.15 (0.17), residues: 1059

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 437 
 TYR   0.020   0.002   TYR A 217 
 PHE   0.018   0.002   PHE C  80 
 TRP   0.010   0.002   TRP B 520 
 HIS   0.003   0.001   HIS C 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 (12118)
  covalent geometry    : angle       0.68594 (16612)
  hydrogen bonds       : bond        0.04555 (  305)
  hydrogen bonds       : angle       5.54338 (  786)

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

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

  3046 Ramachandran restraints generated.
    1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3046 Ramachandran restraints generated.
    1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 92
    poor density    : 150
  time to evaluate  : 0.382 
Fit side-chains
REVERT: A  238 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.7057 (mtp85)
REVERT: A  338 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7320 (mm-30)
REVERT: A  340 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.7037 (tp40)
REVERT: B   22 VAL cc_start: 0.7953 (OUTLIER) cc_final: 0.7727 (t)
REVERT: B  367 GLN cc_start: 0.6803 (OUTLIER) cc_final: 0.6483 (mt0)
REVERT: C  175 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7921 (tp40)
REVERT: C  289 PHE cc_start: 0.8200 (p90) cc_final: 0.7950 (p90)
REVERT: C  390 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.6659 (ttp-170)
REVERT: C  416 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7649 (pp)
  outliers start: 92
  outliers final: 53
  residues processed: 216
  average time/residue: 0.5770
  time to fit residues: 135.1756
Evaluate side-chains
  211 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 150
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  214 ASN
Chi-restraints excluded: chain A residue  238 ARG
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  344 THR
Chi-restraints excluded: chain A residue  351 LYS
Chi-restraints excluded: chain A residue  357 MET
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  438 GLN
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue   98 MET
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  106 MET
Chi-restraints excluded: chain B residue  138 THR
Chi-restraints excluded: chain B residue  148 MET
Chi-restraints excluded: chain B residue  174 ASP
Chi-restraints excluded: chain B residue  193 SER
Chi-restraints excluded: chain B residue  196 ASP
Chi-restraints excluded: chain B residue  238 ARG
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  315 SER
Chi-restraints excluded: chain B residue  344 THR
Chi-restraints excluded: chain B residue  367 GLN
Chi-restraints excluded: chain B residue  378 VAL
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  463 SER
Chi-restraints excluded: chain B residue  529 SER
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  158 GLN
Chi-restraints excluded: chain C residue  175 GLN
Chi-restraints excluded: chain C residue  279 THR
Chi-restraints excluded: chain C residue  308 THR
Chi-restraints excluded: chain C residue  336 GLU
Chi-restraints excluded: chain C residue  353 THR
Chi-restraints excluded: chain C residue  374 VAL
Chi-restraints excluded: chain C residue  390 ARG
Chi-restraints excluded: chain C residue  416 LEU
Chi-restraints excluded: chain C residue  499 LEU
Chi-restraints excluded: chain C residue  508 THR
Chi-restraints excluded: chain C residue  511 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 45 optimal weight:   20.0000
   chunk 112 optimal weight:    0.4980
   chunk 52 optimal weight:    3.9990
   chunk 127 optimal weight:   20.0000
   chunk 33 optimal weight:    9.9990
   chunk 109 optimal weight:    2.9990
   chunk 76 optimal weight:    9.9990
   chunk 129 optimal weight:   50.0000
   chunk 15 optimal weight:    8.9990
   chunk 119 optimal weight:    8.9990
   chunk 42 optimal weight:   30.0000
   overall best weight:    5.0988

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

Flipped N/Q/H residues before XYZ refinement:
A 261 ASN
A 402 GLN
B 261 ASN
B 334 GLN
B 367 GLN
B 402 GLN
C 479 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.178528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.112229 restraints weight = 11969.316|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 1.49
r_work: 0.3209 rms_B_bonded: 1.51 restraints_weight: 0.5000
r_work: 0.3127 rms_B_bonded: 2.45 restraints_weight: 0.2500
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.0674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069  12118  Z= 0.188
  Angle     :  0.722  12.185  16612  Z= 0.370
  Chirality :  0.050   0.230   1892
  Planarity :  0.007   0.142   2174
  Dihedral  :  8.324  59.317   1704
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  5.58 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  6.37 %
    Allowed  : 20.28 %
    Favored  : 73.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    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: -1.21 (0.19), residues: 1523
  helix: -0.96 (0.64), residues: 52
  sheet:  0.02 (0.24), residues: 412
  loop : -1.20 (0.17), residues: 1059

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 152 
 TYR   0.022   0.002   TYR A 217 
 PHE   0.017   0.002   PHE C  80 
 TRP   0.010   0.002   TRP C 169 
 HIS   0.003   0.001   HIS C 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 (12118)
  covalent geometry    : angle       0.72168 (16612)
  hydrogen bonds       : bond        0.04548 (  305)
  hydrogen bonds       : angle       5.52036 (  786)

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

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

  3046 Ramachandran restraints generated.
    1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3046 Ramachandran restraints generated.
    1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 81
    poor density    : 151
  time to evaluate  : 0.436 
Fit side-chains
REVERT: A  100 THR cc_start: 0.8969 (OUTLIER) cc_final: 0.8435 (m)
REVERT: A  224 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.6889 (mtt-85)
REVERT: A  238 ARG cc_start: 0.7299 (OUTLIER) cc_final: 0.7041 (mtp85)
REVERT: A  338 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7250 (mm-30)
REVERT: A  340 GLN cc_start: 0.7638 (OUTLIER) cc_final: 0.6999 (tp40)
REVERT: B   22 VAL cc_start: 0.7941 (OUTLIER) cc_final: 0.7689 (t)
REVERT: B  342 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.7093 (tt0)
REVERT: B  367 GLN cc_start: 0.6953 (OUTLIER) cc_final: 0.6653 (mt0)
REVERT: C  289 PHE cc_start: 0.8160 (p90) cc_final: 0.7930 (p90)
REVERT: C  390 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6695 (ttp-170)
  outliers start: 81
  outliers final: 52
  residues processed: 206
  average time/residue: 0.5478
  time to fit residues: 122.5664
Evaluate side-chains
  208 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 147
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  224 ARG
Chi-restraints excluded: chain A residue  238 ARG
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  344 THR
Chi-restraints excluded: chain A residue  351 LYS
Chi-restraints excluded: chain A residue  357 MET
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  438 GLN
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   98 MET
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  138 THR
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain B residue  148 MET
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  174 ASP
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain B residue  193 SER
Chi-restraints excluded: chain B residue  196 ASP
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  315 SER
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain B residue  367 GLN
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  511 THR
Chi-restraints excluded: chain B residue  529 SER
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   68 SER
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  158 GLN
Chi-restraints excluded: chain C residue  175 GLN
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain C residue  279 THR
Chi-restraints excluded: chain C residue  308 THR
Chi-restraints excluded: chain C residue  353 THR
Chi-restraints excluded: chain C residue  374 VAL
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  390 ARG
Chi-restraints excluded: chain C residue  485 LEU
Chi-restraints excluded: chain C residue  499 LEU
Chi-restraints excluded: chain C residue  508 THR
Chi-restraints excluded: chain C residue  511 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 65 optimal weight:    9.9990
   chunk 139 optimal weight:   30.0000
   chunk 110 optimal weight:    1.9990
   chunk 31 optimal weight:   20.0000
   chunk 125 optimal weight:    3.9990
   chunk 18 optimal weight:    5.9990
   chunk 25 optimal weight:    0.1980
   chunk 105 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 95 optimal weight:    7.9990
   chunk 119 optimal weight:    5.9990
   overall best weight:    2.5986

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

Flipped N/Q/H residues before XYZ refinement:
A 261 ASN
A 402 GLN
B 261 ASN
B 367 GLN
B 402 GLN
C 479 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.180250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.114379 restraints weight = 11953.133|
|-----------------------------------------------------------------------------|
r_work (start): 0.3292 rms_B_bonded: 1.48
r_work: 0.3237 rms_B_bonded: 1.50 restraints_weight: 0.5000
r_work: 0.3156 rms_B_bonded: 2.43 restraints_weight: 0.2500
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.0615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.075  12118  Z= 0.124
  Angle     :  0.630  11.260  16612  Z= 0.321
  Chirality :  0.046   0.222   1892
  Planarity :  0.007   0.141   2174
  Dihedral  :  7.611  58.349   1694
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 3.07
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  5.58 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  6.05 %
    Allowed  : 20.68 %
    Favored  : 73.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -1.09 (0.20), residues: 1523
  helix: -0.81 (0.65), residues: 52
  sheet:  0.07 (0.24), residues: 418
  loop : -1.11 (0.18), residues: 1053

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 478 
 TYR   0.016   0.001   TYR A 217 
 PHE   0.019   0.002   PHE C  80 
 TRP   0.010   0.001   TRP C 169 
 HIS   0.002   0.001   HIS C 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (12118)
  covalent geometry    : angle       0.62966 (16612)
  hydrogen bonds       : bond        0.03742 (  305)
  hydrogen bonds       : angle       5.33461 (  786)

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

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

  3046 Ramachandran restraints generated.
    1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3046 Ramachandran restraints generated.
    1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 150
  time to evaluate  : 0.387 
Fit side-chains
REVERT: A  224 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.6867 (mtt-85)
REVERT: A  238 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.7033 (mtp85)
REVERT: A  340 GLN cc_start: 0.7528 (OUTLIER) cc_final: 0.6892 (tp40)
REVERT: B   20 ASP cc_start: 0.7382 (OUTLIER) cc_final: 0.6879 (p0)
REVERT: B   22 VAL cc_start: 0.7861 (OUTLIER) cc_final: 0.7652 (t)
REVERT: B  166 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.8438 (ptt90)
REVERT: B  254 VAL cc_start: 0.8460 (OUTLIER) cc_final: 0.8229 (p)
REVERT: B  367 GLN cc_start: 0.6796 (OUTLIER) cc_final: 0.6404 (mt0)
REVERT: C  175 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7899 (tp40)
REVERT: C  289 PHE cc_start: 0.8154 (p90) cc_final: 0.7951 (p90)
REVERT: C  390 ARG cc_start: 0.7121 (OUTLIER) cc_final: 0.6678 (ttp-170)
REVERT: C  416 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7538 (pp)
  outliers start: 77
  outliers final: 42
  residues processed: 201
  average time/residue: 0.5960
  time to fit residues: 129.8591
Evaluate side-chains
  202 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 149
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  149 CYS
Chi-restraints excluded: chain A residue  224 ARG
Chi-restraints excluded: chain A residue  238 ARG
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  344 THR
Chi-restraints excluded: chain A residue  351 LYS
Chi-restraints excluded: chain A residue  357 MET
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  516 GLU
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   28 GLN
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue   98 MET
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  106 MET
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain B residue  148 MET
Chi-restraints excluded: chain B residue  166 ARG
Chi-restraints excluded: chain B residue  196 ASP
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  315 SER
Chi-restraints excluded: chain B residue  341 THR
Chi-restraints excluded: chain B residue  367 GLN
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   68 SER
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  158 GLN
Chi-restraints excluded: chain C residue  175 GLN
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain C residue  308 THR
Chi-restraints excluded: chain C residue  353 THR
Chi-restraints excluded: chain C residue  357 MET
Chi-restraints excluded: chain C residue  374 VAL
Chi-restraints excluded: chain C residue  390 ARG
Chi-restraints excluded: chain C residue  416 LEU
Chi-restraints excluded: chain C residue  485 LEU
Chi-restraints excluded: chain C residue  499 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 104 optimal weight:    2.9990
   chunk 1 optimal weight:    8.9990
   chunk 3 optimal weight:    5.9990
   chunk 121 optimal weight:    8.9990
   chunk 95 optimal weight:    5.9990
   chunk 148 optimal weight:    8.9990
   chunk 28 optimal weight:   50.0000
   chunk 107 optimal weight:   10.0000
   chunk 100 optimal weight:   20.0000
   chunk 86 optimal weight:   30.0000
   chunk 44 optimal weight:   10.0000
   overall best weight:    6.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 261 ASN
A 402 GLN
B 261 ASN
B 334 GLN
B 402 GLN
C 479 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.177838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.115389 restraints weight = 11846.390|
|-----------------------------------------------------------------------------|
r_work (start): 0.3303 rms_B_bonded: 1.72
r_work: 0.3193 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3110 rms_B_bonded: 3.10 restraints_weight: 0.2500
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.0817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.064  12118  Z= 0.230
  Angle     :  0.780  12.692  16612  Z= 0.398
  Chirality :  0.052   0.234   1892
  Planarity :  0.008   0.144   2174
  Dihedral  :  7.722  58.450   1684
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  5.71 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  6.84 %
    Allowed  : 20.20 %
    Favored  : 72.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    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: -1.27 (0.19), residues: 1523
  helix: -1.07 (0.64), residues: 52
  sheet:  0.00 (0.24), residues: 409
  loop : -1.24 (0.17), residues: 1062

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 180 
 TYR   0.026   0.002   TYR A 217 
 PHE   0.017   0.003   PHE B  59 
 TRP   0.010   0.002   TRP C 169 
 HIS   0.005   0.001   HIS C 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00572 (12118)
  covalent geometry    : angle       0.78003 (16612)
  hydrogen bonds       : bond        0.04790 (  305)
  hydrogen bonds       : angle       5.52187 (  786)

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

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

  3046 Ramachandran restraints generated.
    1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3046 Ramachandran restraints generated.
    1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 87
    poor density    : 151
  time to evaluate  : 0.499 
Fit side-chains
REVERT: A  107 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8725 (mt-10)
REVERT: A  238 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.7077 (mtp85)
REVERT: A  340 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7072 (tt0)
REVERT: B   20 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.7054 (p0)
REVERT: B   22 VAL cc_start: 0.7985 (OUTLIER) cc_final: 0.7702 (t)
REVERT: B   28 GLN cc_start: 0.6280 (OUTLIER) cc_final: 0.5716 (mm-40)
REVERT: B  166 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8367 (ptt90)
REVERT: C  289 PHE cc_start: 0.8337 (p90) cc_final: 0.8106 (p90)
REVERT: C  292 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6145 (mm-30)
REVERT: C  390 ARG cc_start: 0.7198 (OUTLIER) cc_final: 0.6273 (ttp-170)
REVERT: C  416 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7718 (pp)
  outliers start: 87
  outliers final: 55
  residues processed: 214
  average time/residue: 0.5715
  time to fit residues: 132.7173
Evaluate side-chains
  213 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 148
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  107 GLU
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  214 ASN
Chi-restraints excluded: chain A residue  238 ARG
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  344 THR
Chi-restraints excluded: chain A residue  351 LYS
Chi-restraints excluded: chain A residue  357 MET
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   28 GLN
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue   98 MET
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  138 THR
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain B residue  148 MET
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  166 ARG
Chi-restraints excluded: chain B residue  174 ASP
Chi-restraints excluded: chain B residue  193 SER
Chi-restraints excluded: chain B residue  196 ASP
Chi-restraints excluded: chain B residue  238 ARG
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  315 SER
Chi-restraints excluded: chain B residue  341 THR
Chi-restraints excluded: chain B residue  351 LYS
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  511 THR
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   68 SER
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  158 GLN
Chi-restraints excluded: chain C residue  175 GLN
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain C residue  260 SER
Chi-restraints excluded: chain C residue  279 THR
Chi-restraints excluded: chain C residue  292 GLU
Chi-restraints excluded: chain C residue  303 GLU
Chi-restraints excluded: chain C residue  308 THR
Chi-restraints excluded: chain C residue  336 GLU
Chi-restraints excluded: chain C residue  353 THR
Chi-restraints excluded: chain C residue  374 VAL
Chi-restraints excluded: chain C residue  390 ARG
Chi-restraints excluded: chain C residue  416 LEU
Chi-restraints excluded: chain C residue  485 LEU
Chi-restraints excluded: chain C residue  499 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 37 optimal weight:    8.9990
   chunk 40 optimal weight:    8.9990
   chunk 22 optimal weight:    8.9990
   chunk 120 optimal weight:    7.9990
   chunk 117 optimal weight:    2.9990
   chunk 86 optimal weight:   30.0000
   chunk 27 optimal weight:   30.0000
   chunk 25 optimal weight:   10.0000
   chunk 69 optimal weight:    6.9990
   chunk 12 optimal weight:    0.9990
   chunk 41 optimal weight:    9.9990
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 261 ASN
A 402 GLN
B 261 ASN
B 334 GLN
B 402 GLN
C 479 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.177988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.113117 restraints weight = 11873.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.3274 rms_B_bonded: 1.71
r_work: 0.3201 rms_B_bonded: 1.71 restraints_weight: 0.5000
r_work: 0.3121 rms_B_bonded: 2.79 restraints_weight: 0.2500
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8341
moved from start:          0.0824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.068  12118  Z= 0.203
  Angle     :  0.744  12.435  16612  Z= 0.380
  Chirality :  0.050   0.234   1892
  Planarity :  0.008   0.144   2174
  Dihedral  :  7.695  58.228   1684
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 3.29
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  5.78 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  6.53 %
    Allowed  : 20.52 %
    Favored  : 72.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    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: -1.33 (0.19), residues: 1523
  helix: -1.10 (0.63), residues: 52
  sheet: -0.05 (0.24), residues: 414
  loop : -1.28 (0.17), residues: 1057

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 180 
 TYR   0.023   0.002   TYR A 217 
 PHE   0.016   0.002   PHE C  59 
 TRP   0.010   0.002   TRP C 169 
 HIS   0.004   0.001   HIS C 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00502 (12118)
  covalent geometry    : angle       0.74412 (16612)
  hydrogen bonds       : bond        0.04529 (  305)
  hydrogen bonds       : angle       5.51234 (  786)

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

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

  3046 Ramachandran restraints generated.
    1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3046 Ramachandran restraints generated.
    1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 83
    poor density    : 147
  time to evaluate  : 0.475 
Fit side-chains
REVERT: A  100 THR cc_start: 0.8995 (OUTLIER) cc_final: 0.8470 (m)
REVERT: A  238 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.7096 (mtp85)
REVERT: A  340 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.7008 (tt0)
REVERT: B   20 ASP cc_start: 0.7498 (OUTLIER) cc_final: 0.6915 (p0)
REVERT: B   22 VAL cc_start: 0.7985 (OUTLIER) cc_final: 0.7716 (t)
REVERT: B  166 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.8426 (ptt90)
REVERT: C  155 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8057 (mp0)
REVERT: C  289 PHE cc_start: 0.8266 (p90) cc_final: 0.8036 (p90)
REVERT: C  292 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6065 (mm-30)
REVERT: C  390 ARG cc_start: 0.7178 (OUTLIER) cc_final: 0.6216 (ttp-170)
REVERT: C  416 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7622 (pp)
  outliers start: 83
  outliers final: 57
  residues processed: 206
  average time/residue: 0.5870
  time to fit residues: 131.4876
Evaluate side-chains
  214 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 147
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  214 ASN
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  238 ARG
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  344 THR
Chi-restraints excluded: chain A residue  351 LYS
Chi-restraints excluded: chain A residue  357 MET
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   28 GLN
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue   98 MET
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  106 MET
Chi-restraints excluded: chain B residue  138 THR
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain B residue  148 MET
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  166 ARG
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain B residue  193 SER
Chi-restraints excluded: chain B residue  196 ASP
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  315 SER
Chi-restraints excluded: chain B residue  341 THR
Chi-restraints excluded: chain B residue  374 VAL
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  511 THR
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   68 SER
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  155 GLU
Chi-restraints excluded: chain C residue  158 GLN
Chi-restraints excluded: chain C residue  175 GLN
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain C residue  260 SER
Chi-restraints excluded: chain C residue  292 GLU
Chi-restraints excluded: chain C residue  303 GLU
Chi-restraints excluded: chain C residue  353 THR
Chi-restraints excluded: chain C residue  357 MET
Chi-restraints excluded: chain C residue  374 VAL
Chi-restraints excluded: chain C residue  390 ARG
Chi-restraints excluded: chain C residue  416 LEU
Chi-restraints excluded: chain C residue  485 LEU
Chi-restraints excluded: chain C residue  499 LEU
Chi-restraints excluded: chain C residue  508 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 142 optimal weight:    8.9990
   chunk 1 optimal weight:    6.9990
   chunk 53 optimal weight:    0.7980
   chunk 82 optimal weight:    3.9990
   chunk 108 optimal weight:    1.9990
   chunk 99 optimal weight:    7.9990
   chunk 139 optimal weight:    8.9990
   chunk 22 optimal weight:    6.9990
   chunk 109 optimal weight:    0.7980
   chunk 147 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
A 261 ASN
A 402 GLN
B 261 ASN
B 402 GLN
C 479 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.180776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.115157 restraints weight = 11956.537|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 1.49
r_work: 0.3247 rms_B_bonded: 1.51 restraints_weight: 0.5000
r_work: 0.3166 rms_B_bonded: 2.46 restraints_weight: 0.2500
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.0736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.078  12118  Z= 0.109
  Angle     :  0.613  11.723  16612  Z= 0.311
  Chirality :  0.045   0.219   1892
  Planarity :  0.007   0.141   2174
  Dihedral  :  7.071  57.124   1683
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  5.38 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 21.78 %
    Favored  : 73.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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 (0.20), residues: 1523
  helix: -0.78 (0.65), residues: 52
  sheet:  0.02 (0.24), residues: 419
  loop : -1.11 (0.18), residues: 1052

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  72 
 TYR   0.016   0.001   TYR A 217 
 PHE   0.019   0.001   PHE C  80 
 TRP   0.010   0.001   TRP B 520 
 HIS   0.002   0.001   HIS C 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 (12118)
  covalent geometry    : angle       0.61347 (16612)
  hydrogen bonds       : bond        0.03468 (  305)
  hydrogen bonds       : angle       5.24158 (  786)

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

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

  3046 Ramachandran restraints generated.
    1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3046 Ramachandran restraints generated.
    1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 151
  time to evaluate  : 0.469 
Fit side-chains
REVERT: A  238 ARG cc_start: 0.7226 (OUTLIER) cc_final: 0.7004 (mtp85)
REVERT: B   20 ASP cc_start: 0.7330 (OUTLIER) cc_final: 0.6777 (p0)
REVERT: B  166 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.8432 (ptt90)
REVERT: C  155 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7992 (mp0)
REVERT: C  175 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7883 (tp40)
REVERT: C  390 ARG cc_start: 0.7081 (OUTLIER) cc_final: 0.6625 (ttp-170)
REVERT: C  416 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7519 (pp)
  outliers start: 66
  outliers final: 44
  residues processed: 197
  average time/residue: 0.5818
  time to fit residues: 124.2566
Evaluate side-chains
  198 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 147
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  149 CYS
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  214 ASN
Chi-restraints excluded: chain A residue  238 ARG
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  344 THR
Chi-restraints excluded: chain A residue  351 LYS
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   28 GLN
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue   98 MET
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  106 MET
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain B residue  148 MET
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  166 ARG
Chi-restraints excluded: chain B residue  193 SER
Chi-restraints excluded: chain B residue  196 ASP
Chi-restraints excluded: chain B residue  315 SER
Chi-restraints excluded: chain B residue  341 THR
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   68 SER
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  155 GLU
Chi-restraints excluded: chain C residue  175 GLN
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain C residue  207 SER
Chi-restraints excluded: chain C residue  260 SER
Chi-restraints excluded: chain C residue  303 GLU
Chi-restraints excluded: chain C residue  353 THR
Chi-restraints excluded: chain C residue  357 MET
Chi-restraints excluded: chain C residue  374 VAL
Chi-restraints excluded: chain C residue  390 ARG
Chi-restraints excluded: chain C residue  416 LEU
Chi-restraints excluded: chain C residue  485 LEU
Chi-restraints excluded: chain C residue  508 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 99 optimal weight:   20.0000
   chunk 45 optimal weight:    8.9990
   chunk 49 optimal weight:    5.9990
   chunk 39 optimal weight:   20.0000
   chunk 48 optimal weight:   20.0000
   chunk 21 optimal weight:    3.9990
   chunk 88 optimal weight:   30.0000
   chunk 4 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 138 optimal weight:   40.0000
   chunk 107 optimal weight:    9.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 261 ASN
A 402 GLN
B 261 ASN
B 402 GLN
C 479 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.178571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 80)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.114427 restraints weight = 11864.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.3299 rms_B_bonded: 1.61
r_work: 0.3222 rms_B_bonded: 1.65 restraints_weight: 0.5000
r_work: 0.3142 rms_B_bonded: 2.72 restraints_weight: 0.2500
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
moved from start:          0.0813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068  12118  Z= 0.180
  Angle     :  0.716  12.221  16612  Z= 0.363
  Chirality :  0.049   0.231   1892
  Planarity :  0.007   0.143   2174
  Dihedral  :  6.888  56.830   1674
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  5.45 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  5.27 %
    Allowed  : 21.93 %
    Favored  : 72.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    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: -1.20 (0.20), residues: 1523
  helix: -0.96 (0.64), residues: 52
  sheet: -0.02 (0.24), residues: 414
  loop : -1.17 (0.17), residues: 1057

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 180 
 TYR   0.023   0.002   TYR A 217 
 PHE   0.016   0.002   PHE C  80 
 TRP   0.010   0.002   TRP C 169 
 HIS   0.004   0.001   HIS C 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 (12118)
  covalent geometry    : angle       0.71641 (16612)
  hydrogen bonds       : bond        0.04254 (  305)
  hydrogen bonds       : angle       5.36051 (  786)

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

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

  3046 Ramachandran restraints generated.
    1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3046 Ramachandran restraints generated.
    1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 145
  time to evaluate  : 0.476 
Fit side-chains
REVERT: A  238 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.7096 (mtp85)
REVERT: A  340 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.6956 (tp40)
REVERT: B   20 ASP cc_start: 0.7450 (OUTLIER) cc_final: 0.6877 (p0)
REVERT: B   22 VAL cc_start: 0.7966 (OUTLIER) cc_final: 0.7719 (t)
REVERT: B  166 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8337 (ptt90)
REVERT: B  512 ASP cc_start: 0.7725 (m-30) cc_final: 0.7282 (m-30)
REVERT: C  155 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8097 (mp0)
REVERT: C  175 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7888 (tp40)
REVERT: C  390 ARG cc_start: 0.7166 (OUTLIER) cc_final: 0.6678 (ttp-170)
  outliers start: 67
  outliers final: 49
  residues processed: 196
  average time/residue: 0.5683
  time to fit residues: 120.6786
Evaluate side-chains
  198 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 141
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  214 ASN
Chi-restraints excluded: chain A residue  238 ARG
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  344 THR
Chi-restraints excluded: chain A residue  351 LYS
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   28 GLN
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue   98 MET
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  106 MET
Chi-restraints excluded: chain B residue  138 THR
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain B residue  148 MET
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  166 ARG
Chi-restraints excluded: chain B residue  193 SER
Chi-restraints excluded: chain B residue  196 ASP
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  315 SER
Chi-restraints excluded: chain B residue  341 THR
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain B residue  511 THR
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   68 SER
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  155 GLU
Chi-restraints excluded: chain C residue  175 GLN
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain C residue  207 SER
Chi-restraints excluded: chain C residue  260 SER
Chi-restraints excluded: chain C residue  303 GLU
Chi-restraints excluded: chain C residue  353 THR
Chi-restraints excluded: chain C residue  357 MET
Chi-restraints excluded: chain C residue  374 VAL
Chi-restraints excluded: chain C residue  390 ARG
Chi-restraints excluded: chain C residue  485 LEU
Chi-restraints excluded: chain C residue  508 THR
Chi-restraints excluded: chain C residue  511 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 27 optimal weight:   20.0000
   chunk 141 optimal weight:    4.9990
   chunk 104 optimal weight:    2.9990
   chunk 4 optimal weight:    6.9990
   chunk 149 optimal weight:   20.0000
   chunk 73 optimal weight:    1.9990
   chunk 151 optimal weight:    3.9990
   chunk 44 optimal weight:   10.0000
   chunk 113 optimal weight:    0.9990
   chunk 111 optimal weight:    1.9990
   chunk 97 optimal weight:    7.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 261 ASN
A 402 GLN
B 261 ASN
B 402 GLN
C 479 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.180433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.115437 restraints weight = 11758.917|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 1.66
r_work: 0.3236 rms_B_bonded: 1.66 restraints_weight: 0.5000
r_work: 0.3155 rms_B_bonded: 2.70 restraints_weight: 0.2500
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.0777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077  12118  Z= 0.120
  Angle     :  0.634  11.397  16612  Z= 0.320
  Chirality :  0.046   0.221   1892
  Planarity :  0.007   0.141   2174
  Dihedral  :  6.545  55.776   1674
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  5.38 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 22.41 %
    Favored  : 72.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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 (0.20), residues: 1523
  helix: -0.76 (0.65), residues: 52
  sheet:  0.03 (0.24), residues: 419
  loop : -1.10 (0.18), residues: 1052

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 478 
 TYR   0.016   0.001   TYR A 217 
 PHE   0.019   0.001   PHE C  80 
 TRP   0.010   0.001   TRP C 169 
 HIS   0.003   0.001   HIS C 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 (12118)
  covalent geometry    : angle       0.63407 (16612)
  hydrogen bonds       : bond        0.03591 (  305)
  hydrogen bonds       : angle       5.21814 (  786)

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

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

  3046 Ramachandran restraints generated.
    1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3046 Ramachandran restraints generated.
    1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 148
  time to evaluate  : 0.423 
Fit side-chains
REVERT: A  238 ARG cc_start: 0.7239 (OUTLIER) cc_final: 0.7016 (mtp85)
REVERT: A  340 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.6870 (tp40)
REVERT: B   20 ASP cc_start: 0.7393 (OUTLIER) cc_final: 0.6853 (p0)
REVERT: B  166 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8445 (ptt90)
REVERT: B  512 ASP cc_start: 0.7664 (m-30) cc_final: 0.7249 (m-30)
REVERT: C  155 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8054 (mp0)
REVERT: C  175 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7888 (tp40)
REVERT: C  390 ARG cc_start: 0.7071 (OUTLIER) cc_final: 0.6585 (ttp-170)
  outliers start: 59
  outliers final: 45
  residues processed: 189
  average time/residue: 0.6019
  time to fit residues: 123.5229
Evaluate side-chains
  197 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 145
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  214 ASN
Chi-restraints excluded: chain A residue  238 ARG
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  339 ILE
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  344 THR
Chi-restraints excluded: chain A residue  351 LYS
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain B residue   17 SER
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   28 GLN
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue   98 MET
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  106 MET
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain B residue  148 MET
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  166 ARG
Chi-restraints excluded: chain B residue  193 SER
Chi-restraints excluded: chain B residue  196 ASP
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  315 SER
Chi-restraints excluded: chain B residue  341 THR
Chi-restraints excluded: chain B residue  405 ILE
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   68 SER
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  155 GLU
Chi-restraints excluded: chain C residue  175 GLN
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain C residue  207 SER
Chi-restraints excluded: chain C residue  260 SER
Chi-restraints excluded: chain C residue  303 GLU
Chi-restraints excluded: chain C residue  353 THR
Chi-restraints excluded: chain C residue  357 MET
Chi-restraints excluded: chain C residue  374 VAL
Chi-restraints excluded: chain C residue  390 ARG
Chi-restraints excluded: chain C residue  485 LEU
Chi-restraints excluded: chain C residue  508 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 98 optimal weight:    8.9990
   chunk 1 optimal weight:    0.5980
   chunk 83 optimal weight:    0.0370
   chunk 122 optimal weight:   10.0000
   chunk 145 optimal weight:    7.9990
   chunk 105 optimal weight:    9.9990
   chunk 13 optimal weight:    0.5980
   chunk 59 optimal weight:    5.9990
   chunk 112 optimal weight:    0.9980
   chunk 110 optimal weight:    9.9990
   chunk 146 optimal weight:    0.9990
   overall best weight:    0.6460

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

Flipped N/Q/H residues before XYZ refinement:
A 261 ASN
A 371 GLN
A 402 GLN
B 402 GLN
C 479 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.184280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.121092 restraints weight = 12040.394|
|-----------------------------------------------------------------------------|
r_work (start): 0.3378 rms_B_bonded: 1.70
r_work: 0.3298 rms_B_bonded: 1.71 restraints_weight: 0.5000
r_work: 0.3218 rms_B_bonded: 2.80 restraints_weight: 0.2500
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.1029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.079  12118  Z= 0.090
  Angle     :  0.569  12.394  16612  Z= 0.283
  Chirality :  0.044   0.226   1892
  Planarity :  0.006   0.139   2174
  Dihedral  :  5.887  52.994   1673
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.25 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 23.82 %
    Favored  : 72.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    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: -0.91 (0.20), residues: 1523
  helix: -0.28 (0.67), residues: 52
  sheet:  0.09 (0.24), residues: 416
  loop : -0.95 (0.18), residues: 1055

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 478 
 TYR   0.008   0.001   TYR A 217 
 PHE   0.020   0.001   PHE C  80 
 TRP   0.013   0.001   TRP A 520 
 HIS   0.002   0.001   HIS A 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00211 (12118)
  covalent geometry    : angle       0.56898 (16612)
  hydrogen bonds       : bond        0.02855 (  305)
  hydrogen bonds       : angle       4.99088 (  786)

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

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

  3046 Ramachandran restraints generated.
    1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3046 Ramachandran restraints generated.
    1523 Oldfield, 0 Emsley, 1523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 156
  time to evaluate  : 0.334 
Fit side-chains
REVERT: A  357 MET cc_start: 0.8080 (ttt) cc_final: 0.7705 (ttt)
REVERT: A  456 GLU cc_start: 0.7261 (mp0) cc_final: 0.6927 (mp0)
REVERT: B   64 LEU cc_start: 0.8413 (tt) cc_final: 0.8199 (tt)
REVERT: C  155 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.8007 (mp0)
REVERT: C  175 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7844 (tp40)
REVERT: C  207 SER cc_start: 0.9009 (OUTLIER) cc_final: 0.8731 (t)
REVERT: C  390 ARG cc_start: 0.6968 (OUTLIER) cc_final: 0.6350 (ttp-170)
  outliers start: 42
  outliers final: 24
  residues processed: 183
  average time/residue: 0.6110
  time to fit residues: 121.1313
Evaluate side-chains
  178 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 150
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  344 THR
Chi-restraints excluded: chain A residue  351 LYS
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue   98 MET
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  141 ILE
Chi-restraints excluded: chain B residue  148 MET
Chi-restraints excluded: chain B residue  193 SER
Chi-restraints excluded: chain B residue  315 SER
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  155 GLU
Chi-restraints excluded: chain C residue  175 GLN
Chi-restraints excluded: chain C residue  207 SER
Chi-restraints excluded: chain C residue  260 SER
Chi-restraints excluded: chain C residue  357 MET
Chi-restraints excluded: chain C residue  390 ARG
Chi-restraints excluded: chain C residue  485 LEU
Chi-restraints excluded: chain C residue  508 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 49 optimal weight:   20.0000
   chunk 129 optimal weight:   40.0000
   chunk 151 optimal weight:   20.0000
   chunk 47 optimal weight:   10.0000
   chunk 3 optimal weight:    2.9990
   chunk 108 optimal weight:    9.9990
   chunk 140 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 97 optimal weight:   20.0000
   chunk 35 optimal weight:    6.9990
   chunk 21 optimal weight:    7.9990
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 261 ASN
A 371 GLN
A 402 GLN
A 479 ASN
B 334 GLN
B 402 GLN
C 479 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.178734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.112699 restraints weight = 11880.821|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 1.46
r_work: 0.3210 rms_B_bonded: 1.49 restraints_weight: 0.5000
r_work: 0.3129 rms_B_bonded: 2.42 restraints_weight: 0.2500
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8290
moved from start:          0.0911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067  12118  Z= 0.208
  Angle     :  0.752  12.349  16612  Z= 0.381
  Chirality :  0.051   0.239   1892
  Planarity :  0.007   0.143   2174
  Dihedral  :  6.238  54.167   1663
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  5.58 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 22.48 %
    Favored  : 73.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.24 %
    Cis-general     : 0.07 %
    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: -1.12 (0.20), residues: 1523
  helix: -0.85 (0.64), residues: 52
  sheet:  0.05 (0.24), residues: 408
  loop : -1.12 (0.18), residues: 1063

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 152 
 TYR   0.024   0.002   TYR A 217 
 PHE   0.016   0.002   PHE B  59 
 TRP   0.009   0.002   TRP C 169 
 HIS   0.003   0.001   HIS C 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00516 (12118)
  covalent geometry    : angle       0.75201 (16612)
  hydrogen bonds       : bond        0.04408 (  305)
  hydrogen bonds       : angle       5.32483 (  786)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5858.21 seconds
wall clock time: 100 minutes 3.53 seconds (6003.53 seconds total)