Starting phenix.real_space_refine
on Sun May 18 05:29:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kjr_62372/05_2025/9kjr_62372.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kjr_62372/05_2025/9kjr_62372.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.86
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kjr_62372/05_2025/9kjr_62372.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kjr_62372/05_2025/9kjr_62372.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kjr_62372/05_2025/9kjr_62372.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kjr_62372/05_2025/9kjr_62372.cif"
  }
  resolution = 3.86
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.021
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: 4
    Type Number    sf(0)   Gaussians
     S      72      5.16       5
     C   10359      2.51       5
     N    2820      2.21       5
     O    3162      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 16413
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 5471
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 710, 5471
          Classifications: {'peptide': 710}
          Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 675}
    Chain: "B"
      Number of atoms: 5471
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 710, 5471
          Classifications: {'peptide': 710}
          Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 675}
    Chain: "C"
      Number of atoms: 5471
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 710, 5471
          Classifications: {'peptide': 710}
          Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 675}
  Time building chain proxies: 10.10, per 1000 atoms: 0.62
  Number of scatterers: 16413
  At special positions: 0
  Unit cell: (108.73, 106.24, 122.84, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      72     16.00
     O    3162      8.00
     N    2820      7.00
     C   10359      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: 4.55
  Conformation dependent library (CDL) restraints added in 2.2 seconds
  

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3960

  Finding SS restraints...
    Secondary structure from input PDB file:
      61 helices and 17 sheets defined
      39.3% alpha, 22.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 124 through 139
    Processing helix  chain 'A' and resid 140 through 142
      No H-bonds generated for 'chain 'A' and resid 140 through 142'
    Processing helix  chain 'A' and resid 165 through 180
    Processing helix  chain 'A' and resid 205 through 212
    Processing helix  chain 'A' and resid 238 through 267
    Processing helix  chain 'A' and resid 280 through 301
      removed outlier: 5.614A  pdb=" N   GLU A 293 " --> pdb=" O   LYS A 289 " (cutoff:3.500A)
      removed outlier: 5.506A  pdb=" N   ARG A 294 " --> pdb=" O   LEU A 290 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ASP A 301 " --> pdb=" O   ALA A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 328
      removed outlier: 3.651A  pdb=" N   ARG A 309 " --> pdb=" O   ASP A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 356
      removed outlier: 3.670A  pdb=" N   ILE A 336 " --> pdb=" O   ASP A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 406
    Processing helix  chain 'A' and resid 409 through 417
      removed outlier: 3.707A  pdb=" N   THR A 413 " --> pdb=" O   ASP A 409 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ILE A 415 " --> pdb=" O   VAL A 411 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   ASN A 416 " --> pdb=" O   ILE A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 435
    Processing helix  chain 'A' and resid 444 through 459
    Processing helix  chain 'A' and resid 460 through 462
      No H-bonds generated for 'chain 'A' and resid 460 through 462'
    Processing helix  chain 'A' and resid 482 through 499
      removed outlier: 3.518A  pdb=" N   GLY A 499 " --> pdb=" O   LEU A 495 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 534 through 541
    Processing helix  chain 'A' and resid 567 through 593
      removed outlier: 3.792A  pdb=" N   VAL A 571 " --> pdb=" O   PRO A 567 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 616 through 622
    Processing helix  chain 'A' and resid 625 through 636
      removed outlier: 3.792A  pdb=" N   THR A 635 " --> pdb=" O   LEU A 631 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 653 through 669
    Processing helix  chain 'A' and resid 719 through 724
      removed outlier: 3.506A  pdb=" N   ALA A 722 " --> pdb=" O   HIS A 719 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   GLY A 724 " --> pdb=" O   THR A 721 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 124 through 139
    Processing helix  chain 'B' and resid 140 through 142
      No H-bonds generated for 'chain 'B' and resid 140 through 142'
    Processing helix  chain 'B' and resid 165 through 179
      removed outlier: 3.536A  pdb=" N   ASN B 171 " --> pdb=" O   VAL B 167 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 212
      removed outlier: 3.589A  pdb=" N   SER B 211 " --> pdb=" O   LYS B 207 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 237 through 267
      removed outlier: 3.510A  pdb=" N   PHE B 241 " --> pdb=" O   LEU B 237 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLN B 254 " --> pdb=" O   LYS B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 280 through 301
      removed outlier: 6.003A  pdb=" N   GLU B 293 " --> pdb=" O   LYS B 289 " (cutoff:3.500A)
      removed outlier: 5.627A  pdb=" N   ARG B 294 " --> pdb=" O   LEU B 290 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ASP B 301 " --> pdb=" O   ALA B 297 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 305 through 328
    Processing helix  chain 'B' and resid 332 through 356
    Processing helix  chain 'B' and resid 401 through 406
    Processing helix  chain 'B' and resid 409 through 417
      removed outlier: 3.531A  pdb=" N   THR B 413 " --> pdb=" O   ASP B 409 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 430 through 435
    Processing helix  chain 'B' and resid 444 through 459
    Processing helix  chain 'B' and resid 460 through 462
      No H-bonds generated for 'chain 'B' and resid 460 through 462'
    Processing helix  chain 'B' and resid 482 through 498
    Processing helix  chain 'B' and resid 534 through 541
    Processing helix  chain 'B' and resid 567 through 591
      removed outlier: 3.789A  pdb=" N   VAL B 571 " --> pdb=" O   PRO B 567 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 613 through 622
      removed outlier: 4.088A  pdb=" N   ALA B 618 " --> pdb=" O   LEU B 614 " (cutoff:3.500A)
      removed outlier: 4.908A  pdb=" N   LYS B 619 " --> pdb=" O   SER B 615 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 625 through 635
    Processing helix  chain 'B' and resid 653 through 669
    Processing helix  chain 'B' and resid 708 through 712
    Processing helix  chain 'B' and resid 719 through 724
    Processing helix  chain 'C' and resid 105 through 109
      removed outlier: 3.831A  pdb=" N   ALA C 108 " --> pdb=" O   LYS C 105 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 124 through 139
    Processing helix  chain 'C' and resid 140 through 142
      No H-bonds generated for 'chain 'C' and resid 140 through 142'
    Processing helix  chain 'C' and resid 165 through 180
    Processing helix  chain 'C' and resid 205 through 212
    Processing helix  chain 'C' and resid 237 through 267
      removed outlier: 3.759A  pdb=" N   PHE C 241 " --> pdb=" O   LEU C 237 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   GLN C 253 " --> pdb=" O   VAL C 249 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   GLN C 254 " --> pdb=" O   LYS C 250 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   ILE C 255 " --> pdb=" O   TYR C 251 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 280 through 301
      removed outlier: 5.881A  pdb=" N   GLU C 293 " --> pdb=" O   LYS C 289 " (cutoff:3.500A)
      removed outlier: 5.468A  pdb=" N   ARG C 294 " --> pdb=" O   LEU C 290 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   ASP C 301 " --> pdb=" O   ALA C 297 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 305 through 328
      removed outlier: 3.586A  pdb=" N   ASP C 319 " --> pdb=" O   LYS C 315 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 332 through 356
    Processing helix  chain 'C' and resid 401 through 406
    Processing helix  chain 'C' and resid 430 through 435
    Processing helix  chain 'C' and resid 444 through 459
    Processing helix  chain 'C' and resid 460 through 462
      No H-bonds generated for 'chain 'C' and resid 460 through 462'
    Processing helix  chain 'C' and resid 482 through 498
    Processing helix  chain 'C' and resid 534 through 541
    Processing helix  chain 'C' and resid 567 through 593
      removed outlier: 3.749A  pdb=" N   VAL C 571 " --> pdb=" O   PRO C 567 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   LYS C 591 " --> pdb=" O   GLN C 587 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   THR C 592 " --> pdb=" O   ILE C 588 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ILE C 593 " --> pdb=" O   MET C 589 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 613 through 622
      removed outlier: 4.372A  pdb=" N   LYS C 619 " --> pdb=" O   SER C 615 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 625 through 636
      removed outlier: 3.780A  pdb=" N   GLU C 634 " --> pdb=" O   LYS C 630 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 653 through 668
    Processing helix  chain 'C' and resid 719 through 724
    Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 51
      removed outlier: 6.490A  pdb=" N   ALA A  79 " --> pdb=" O   LEU A 157 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 199 through 202
      removed outlier: 3.615A  pdb=" N   ILE A 195 " --> pdb=" O   LEU A 214 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   LEU A 214 " --> pdb=" O   ILE A 195 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   ASN A 215 " --> pdb=" O   ALA A 231 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   ALA A 231 " --> pdb=" O   ASN A 215 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   VAL A 217 " --> pdb=" O   LEU A 229 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   LEU A 229 " --> pdb=" O   VAL A 217 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   ALA A 219 " --> pdb=" O   VAL A 227 " (cutoff:3.500A)
      removed outlier: 7.108A  pdb=" N   VAL A 227 " --> pdb=" O   ILE A 561 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   ILE A 561 " --> pdb=" O   VAL A 227 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   LEU A 229 " --> pdb=" O   ALA A 559 " (cutoff:3.500A)
      removed outlier: 4.590A  pdb=" N   THR A 555 " --> pdb=" O   ALA A 233 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   MET A 543 " --> pdb=" O   LEU A 513 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   LEU A 513 " --> pdb=" O   MET A 543 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   ASP A 526 " --> pdb=" O   LYS A 516 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 370 through 374
      removed outlier: 6.280A  pdb=" N   GLN A 392 " --> pdb=" O   LEU A 477 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   MET A 424 " --> pdb=" O   VAL A 472 " (cutoff:3.500A)
      removed outlier: 7.882A  pdb=" N   SER A 474 " --> pdb=" O   MET A 424 " (cutoff:3.500A)
      removed outlier: 6.154A  pdb=" N   HIS A 426 " --> pdb=" O   SER A 474 " (cutoff:3.500A)
      removed outlier: 7.708A  pdb=" N   VAL A 476 " --> pdb=" O   HIS A 426 " (cutoff:3.500A)
      removed outlier: 7.101A  pdb=" N   GLU A 428 " --> pdb=" O   VAL A 476 " (cutoff:3.500A)
      removed outlier: 8.311A  pdb=" N   GLU A 478 " --> pdb=" O   GLU A 428 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 606 through 611
    Processing sheet with id=AA5, first strand: chain 'A' and resid 681 through 686
      removed outlier: 4.072A  pdb=" N   VAL A 705 " --> pdb=" O   VAL A 696 " (cutoff:3.500A)
      removed outlier: 5.091A  pdb=" N   LEU A 706 " --> pdb=" O   MET A 745 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   LEU A 747 " --> pdb=" O   LEU A 706 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   GLY A 737 " --> pdb=" O   ARG A 746 " (cutoff:3.500A)
      removed outlier: 5.762A  pdb=" N   SER A 748 " --> pdb=" O   TYR A 735 " (cutoff:3.500A)
      removed outlier: 5.084A  pdb=" N   TYR A 735 " --> pdb=" O   SER A 748 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.618A  pdb=" N   ALA B  79 " --> pdb=" O   LEU B 157 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   LEU B 156 " --> pdb=" O   ARG B 103 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 199 through 202
      removed outlier: 3.550A  pdb=" N   ILE B 195 " --> pdb=" O   LEU B 214 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   LEU B 214 " --> pdb=" O   ILE B 195 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   ASN B 215 " --> pdb=" O   ALA B 231 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   ALA B 231 " --> pdb=" O   ASN B 215 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   VAL B 217 " --> pdb=" O   LEU B 229 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   LEU B 229 " --> pdb=" O   VAL B 217 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   ALA B 219 " --> pdb=" O   VAL B 227 " (cutoff:3.500A)
      removed outlier: 7.283A  pdb=" N   VAL B 227 " --> pdb=" O   ILE B 561 " (cutoff:3.500A)
      removed outlier: 4.570A  pdb=" N   ILE B 561 " --> pdb=" O   VAL B 227 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   LEU B 229 " --> pdb=" O   ALA B 559 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   THR B 555 " --> pdb=" O   ALA B 233 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   ASN B 235 " --> pdb=" O   GLY B 553 " (cutoff:3.500A)
      removed outlier: 5.580A  pdb=" N   GLY B 553 " --> pdb=" O   ASN B 235 " (cutoff:3.500A)
      removed outlier: 5.711A  pdb=" N   ILE B 554 " --> pdb=" O   THR B 550 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   THR B 550 " --> pdb=" O   ILE B 554 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   MET B 543 " --> pdb=" O   LEU B 513 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   LEU B 513 " --> pdb=" O   MET B 543 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 370 through 374
      removed outlier: 6.487A  pdb=" N   GLN B 392 " --> pdb=" O   LEU B 477 " (cutoff:3.500A)
      removed outlier: 6.357A  pdb=" N   MET B 424 " --> pdb=" O   VAL B 472 " (cutoff:3.500A)
      removed outlier: 7.975A  pdb=" N   SER B 474 " --> pdb=" O   MET B 424 " (cutoff:3.500A)
      removed outlier: 6.027A  pdb=" N   HIS B 426 " --> pdb=" O   SER B 474 " (cutoff:3.500A)
      removed outlier: 7.916A  pdb=" N   VAL B 476 " --> pdb=" O   HIS B 426 " (cutoff:3.500A)
      removed outlier: 7.125A  pdb=" N   GLU B 428 " --> pdb=" O   VAL B 476 " (cutoff:3.500A)
      removed outlier: 8.594A  pdb=" N   GLU B 478 " --> pdb=" O   GLU B 428 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 606 through 611
    Processing sheet with id=AB1, first strand: chain 'B' and resid 705 through 707
    Processing sheet with id=AB2, first strand: chain 'B' and resid 738 through 739
    Processing sheet with id=AB3, first strand: chain 'C' and resid 45 through 51
      removed outlier: 6.479A  pdb=" N   ALA C  79 " --> pdb=" O   LEU C 157 " (cutoff:3.500A)
      removed outlier: 5.314A  pdb=" N   ASP C 149 " --> pdb=" O   LYS C  87 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 199 through 202
      removed outlier: 3.855A  pdb=" N   ILE C 195 " --> pdb=" O   LEU C 214 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   LEU C 214 " --> pdb=" O   ILE C 195 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   ASN C 215 " --> pdb=" O   ALA C 231 " (cutoff:3.500A)
      removed outlier: 4.403A  pdb=" N   ALA C 231 " --> pdb=" O   ASN C 215 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   VAL C 217 " --> pdb=" O   LEU C 229 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   LEU C 229 " --> pdb=" O   VAL C 217 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   ALA C 219 " --> pdb=" O   VAL C 227 " (cutoff:3.500A)
      removed outlier: 6.971A  pdb=" N   VAL C 227 " --> pdb=" O   ILE C 561 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ILE C 561 " --> pdb=" O   VAL C 227 " (cutoff:3.500A)
      removed outlier: 4.559A  pdb=" N   THR C 555 " --> pdb=" O   ALA C 233 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   MET C 543 " --> pdb=" O   LEU C 513 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   LEU C 513 " --> pdb=" O   MET C 543 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   ASP C 526 " --> pdb=" O   LYS C 516 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 370 through 374
      removed outlier: 6.399A  pdb=" N   GLN C 392 " --> pdb=" O   LEU C 477 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   MET C 424 " --> pdb=" O   VAL C 472 " (cutoff:3.500A)
      removed outlier: 7.895A  pdb=" N   SER C 474 " --> pdb=" O   MET C 424 " (cutoff:3.500A)
      removed outlier: 6.249A  pdb=" N   HIS C 426 " --> pdb=" O   SER C 474 " (cutoff:3.500A)
      removed outlier: 7.768A  pdb=" N   VAL C 476 " --> pdb=" O   HIS C 426 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   GLU C 428 " --> pdb=" O   VAL C 476 " (cutoff:3.500A)
      removed outlier: 8.564A  pdb=" N   GLU C 478 " --> pdb=" O   GLU C 428 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 606 through 611
    Processing sheet with id=AB7, first strand: chain 'C' and resid 682 through 685
      removed outlier: 5.433A  pdb=" N   TYR C 735 " --> pdb=" O   SER C 748 " (cutoff:3.500A)
      removed outlier: 7.610A  pdb=" N   SER C 748 " --> pdb=" O   TYR C 735 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   GLY C 737 " --> pdb=" O   ARG C 746 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'C' and resid 695 through 696

    888 hydrogen bonds defined for protein.
    2454 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: 5.92

  Time building geometry restraints manager: 5.23 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: 5494
        1.34 -     1.46: 3338
        1.46 -     1.58: 7722
        1.58 -     1.70: 0
        1.70 -     1.82: 123
  Bond restraints: 16677
  Sorted by residual:
  bond pdb=" CA  SER B 498 "
       pdb=" C   SER B 498 "
    ideal  model  delta    sigma   weight residual
    1.522  1.486  0.035 1.72e-02 3.38e+03 4.24e+00
  bond pdb=" C   GLY B  52 "
       pdb=" N   ASN B  53 "
    ideal  model  delta    sigma   weight residual
    1.332  1.317  0.016 1.40e-02 5.10e+03 1.27e+00
  bond pdb=" CB  MET A 589 "
       pdb=" CG  MET A 589 "
    ideal  model  delta    sigma   weight residual
    1.520  1.490  0.030 3.00e-02 1.11e+03 9.95e-01
  bond pdb=" C   LYS C 562 "
       pdb=" N   LEU C 563 "
    ideal  model  delta    sigma   weight residual
    1.339  1.285  0.054 5.57e-02 3.22e+02 9.56e-01
  bond pdb=" CB  TRP C 184 "
       pdb=" CG  TRP C 184 "
    ideal  model  delta    sigma   weight residual
    1.498  1.468  0.030 3.10e-02 1.04e+03 9.49e-01
  ... (remaining 16672 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.43: 22315
        2.43 -     4.86: 225
        4.86 -     7.29: 22
        7.29 -     9.72: 6
        9.72 -    12.15: 4
  Bond angle restraints: 22572
  Sorted by residual:
  angle pdb=" CB  MET C  44 "
        pdb=" CG  MET C  44 "
        pdb=" SD  MET C  44 "
      ideal   model   delta    sigma   weight residual
     112.70  124.85  -12.15 3.00e+00 1.11e-01 1.64e+01
  angle pdb=" CB  MET C 702 "
        pdb=" CG  MET C 702 "
        pdb=" SD  MET C 702 "
      ideal   model   delta    sigma   weight residual
     112.70  123.83  -11.13 3.00e+00 1.11e-01 1.38e+01
  angle pdb=" CB  MET B 228 "
        pdb=" CG  MET B 228 "
        pdb=" SD  MET B 228 "
      ideal   model   delta    sigma   weight residual
     112.70  123.82  -11.12 3.00e+00 1.11e-01 1.38e+01
  angle pdb=" CB  MET C 292 "
        pdb=" CG  MET C 292 "
        pdb=" SD  MET C 292 "
      ideal   model   delta    sigma   weight residual
     112.70  122.60   -9.90 3.00e+00 1.11e-01 1.09e+01
  angle pdb=" CB  MET B 292 "
        pdb=" CG  MET B 292 "
        pdb=" SD  MET B 292 "
      ideal   model   delta    sigma   weight residual
     112.70  121.97   -9.27 3.00e+00 1.11e-01 9.55e+00
  ... (remaining 22567 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.74: 8809
       17.74 -    35.47: 1064
       35.47 -    53.20: 293
       53.20 -    70.94: 67
       70.94 -    88.67: 45
  Dihedral angle restraints: 10278
    sinusoidal: 4131
      harmonic: 6147
  Sorted by residual:
  dihedral pdb=" CA  PRO C 613 "
           pdb=" C   PRO C 613 "
           pdb=" N   LEU C 614 "
           pdb=" CA  LEU C 614 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.17  -19.83     0      5.00e+00 4.00e-02 1.57e+01
  dihedral pdb=" CA  VAL B 121 "
           pdb=" C   VAL B 121 "
           pdb=" N   GLY B 122 "
           pdb=" CA  GLY B 122 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.35  -19.65     0      5.00e+00 4.00e-02 1.55e+01
  dihedral pdb=" CA  GLN C 104 "
           pdb=" C   GLN C 104 "
           pdb=" N   LYS C 105 "
           pdb=" CA  LYS C 105 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.52   18.48     0      5.00e+00 4.00e-02 1.37e+01
  ... (remaining 10275 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 1602
       0.028 -    0.057: 579
       0.057 -    0.085: 252
       0.085 -    0.113: 163
       0.113 -    0.142: 38
  Chirality restraints: 2634
  Sorted by residual:
  chirality pdb=" CA  VAL C 610 "
            pdb=" N   VAL C 610 "
            pdb=" C   VAL C 610 "
            pdb=" CB  VAL C 610 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 5.02e-01
  chirality pdb=" CA  ILE B 689 "
            pdb=" N   ILE B 689 "
            pdb=" C   ILE B 689 "
            pdb=" CB  ILE B 689 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.52e-01
  chirality pdb=" CA  ILE A 462 "
            pdb=" N   ILE A 462 "
            pdb=" C   ILE A 462 "
            pdb=" CB  ILE A 462 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.24e-01
  ... (remaining 2631 not shown)

  Planarity restraints: 2931
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C 595 "   -0.034 5.00e-02 4.00e+02   5.29e-02 4.47e+00
        pdb=" N   PRO C 596 "    0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO C 596 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO C 596 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET B 745 "   -0.009 2.00e-02 2.50e+03   1.82e-02 3.32e+00
        pdb=" C   MET B 745 "    0.031 2.00e-02 2.50e+03
        pdb=" O   MET B 745 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   ARG B 746 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 699 "    0.025 5.00e-02 4.00e+02   3.80e-02 2.31e+00
        pdb=" N   PRO A 700 "   -0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO A 700 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 700 "    0.021 5.00e-02 4.00e+02
  ... (remaining 2928 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 2745
        2.76 -     3.29: 17577
        3.29 -     3.83: 28970
        3.83 -     4.36: 31360
        4.36 -     4.90: 54048
  Nonbonded interactions: 134700
  Sorted by model distance:
  nonbonded pdb=" OG  SER C 615 "
            pdb=" O   PRO C 740 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" O   GLN A 576 "
            pdb=" OG  SER A 579 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" OH  TYR A 427 "
            pdb=" OG  SER A 483 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" O   THR B 550 "
            pdb=" NZ  LYS B 582 "
     model   vdw
     2.242 3.120
  nonbonded pdb=" OG1 THR B 515 "
            pdb=" OD2 ASP B 542 "
     model   vdw
     2.248 3.040
  ... (remaining 134695 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.890
  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:             0.010
  Extract box with map and model:          0.720
  Check model and map are aligned:         0.130
  Set scattering table:                    0.170
  Process input model:                     39.840
  Find NCS groups from input model:        0.530
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8866
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      :  0.005   0.054  16677  Z= 0.223
  Angle     :  0.627  12.152  22572  Z= 0.315
  Chirality :  0.042   0.142   2634
  Planarity :  0.004   0.053   2931
  Dihedral  : 17.735  88.674   6318
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 15.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.59 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  : 30.30 %
    Favored  : 69.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.19), residues: 2124
  helix:  2.46 (0.19), residues: 716
  sheet:  0.46 (0.24), residues: 499
  loop : -0.94 (0.22), residues: 909

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP B 184 
 HIS   0.005   0.001   HIS B 708 
 PHE   0.010   0.001   PHE B 736 
 TYR   0.016   0.001   TYR B 334 
 ARG   0.008   0.000   ARG A 749 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13266 (  888)
  hydrogen bonds       : angle       6.16794 ( 2454)
  covalent geometry    : bond        0.00474 (16677)
  covalent geometry    : angle       0.62692 (22572)

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

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

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 59
  time to evaluate  : 1.986 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  209 MET cc_start: 0.9154 (mpp) cc_final: 0.8833 (mpp)
  outliers start: 5
  outliers final: 2
  residues processed: 64
  average time/residue: 0.2575
  time to fit residues: 27.4948
Evaluate side-chains
  61 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 59
  time to evaluate  : 1.826 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  681 VAL
Chi-restraints excluded: chain B residue  653 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 179 optimal weight:    8.9990
   chunk 161 optimal weight:    5.9990
   chunk 89 optimal weight:    6.9990
   chunk 55 optimal weight:    4.9990
   chunk 108 optimal weight:    9.9990
   chunk 86 optimal weight:    5.9990
   chunk 166 optimal weight:    1.9990
   chunk 64 optimal weight:   30.0000
   chunk 101 optimal weight:    5.9990
   chunk 124 optimal weight:    0.8980
   chunk 193 optimal weight:    0.9980
   overall best weight:    2.9786

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

Flipped N/Q/H residues before XYZ refinement:
** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 155 ASN
C 392 GLN
C 632 GLN
** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.063391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2572 r_free = 0.2572 target = 0.042465 restraints weight = 87561.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2618 r_free = 0.2618 target = 0.043765 restraints weight = 53133.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2650 r_free = 0.2650 target = 0.044642 restraints weight = 38360.628|
|-----------------------------------------------------------------------------|
r_work (final): 0.2675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8731
moved from start:          0.0596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  16677  Z= 0.234
  Angle     :  0.589   7.040  22572  Z= 0.305
  Chirality :  0.043   0.140   2634
  Planarity :  0.004   0.060   2931
  Dihedral  :  4.197  27.994   2294
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 28.48 %
    Favored  : 68.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.19), residues: 2124
  helix:  2.44 (0.19), residues: 732
  sheet:  0.44 (0.23), residues: 502
  loop : -0.94 (0.23), residues: 890

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 184 
 HIS   0.004   0.001   HIS A 304 
 PHE   0.011   0.001   PHE A 545 
 TYR   0.017   0.001   TYR B 334 
 ARG   0.007   0.001   ARG A 749 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04526 (  888)
  hydrogen bonds       : angle       5.16730 ( 2454)
  covalent geometry    : bond        0.00506 (16677)
  covalent geometry    : angle       0.58921 (22572)

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

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

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 60
  time to evaluate  : 1.802 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  496 MET cc_start: 0.9296 (tpt) cc_final: 0.8720 (tpp)
REVERT: B  116 TYR cc_start: 0.7215 (OUTLIER) cc_final: 0.6167 (t80)
REVERT: C  184 TRP cc_start: 0.9202 (OUTLIER) cc_final: 0.8744 (t60)
REVERT: C  209 MET cc_start: 0.9226 (mpp) cc_final: 0.8836 (mpp)
REVERT: C  424 MET cc_start: 0.8378 (tmm) cc_final: 0.8141 (tmm)
REVERT: C  577 GLN cc_start: 0.9524 (OUTLIER) cc_final: 0.9034 (mt0)
REVERT: C  695 MET cc_start: 0.1772 (tpt) cc_final: 0.1516 (tpp)
  outliers start: 54
  outliers final: 32
  residues processed: 110
  average time/residue: 0.2355
  time to fit residues: 42.3608
Evaluate side-chains
  92 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 57
  time to evaluate  : 1.803 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 MET
Chi-restraints excluded: chain A residue  138 ILE
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  310 ASP
Chi-restraints excluded: chain A residue  332 ASP
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  681 VAL
Chi-restraints excluded: chain B residue   53 ASN
Chi-restraints excluded: chain B residue   91 SER
Chi-restraints excluded: chain B residue  116 TYR
Chi-restraints excluded: chain B residue  124 SER
Chi-restraints excluded: chain B residue  202 VAL
Chi-restraints excluded: chain B residue  401 SER
Chi-restraints excluded: chain B residue  423 PHE
Chi-restraints excluded: chain B residue  543 MET
Chi-restraints excluded: chain B residue  635 THR
Chi-restraints excluded: chain B residue  717 ILE
Chi-restraints excluded: chain B residue  738 ARG
Chi-restraints excluded: chain C residue   75 SER
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  154 CYS
Chi-restraints excluded: chain C residue  184 TRP
Chi-restraints excluded: chain C residue  213 THR
Chi-restraints excluded: chain C residue  272 THR
Chi-restraints excluded: chain C residue  284 VAL
Chi-restraints excluded: chain C residue  336 ILE
Chi-restraints excluded: chain C residue  397 VAL
Chi-restraints excluded: chain C residue  498 SER
Chi-restraints excluded: chain C residue  577 GLN
Chi-restraints excluded: chain C residue  646 THR
Chi-restraints excluded: chain C residue  653 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 178 optimal weight:    6.9990
   chunk 59 optimal weight:    0.9990
   chunk 143 optimal weight:    8.9990
   chunk 125 optimal weight:    0.8980
   chunk 21 optimal weight:    0.8980
   chunk 116 optimal weight:    0.7980
   chunk 86 optimal weight:    7.9990
   chunk 89 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9980
   chunk 2 optimal weight:    7.9990
   chunk 19 optimal weight:    7.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 426 HIS
C 632 GLN
C 675 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.064888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.2660 r_free = 0.2660 target = 0.039000 restraints weight = 81529.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 70)----------------|
| r_work = 0.2694 r_free = 0.2694 target = 0.040237 restraints weight = 52068.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2721 r_free = 0.2721 target = 0.040966 restraints weight = 39170.110|
|-----------------------------------------------------------------------------|
r_work (final): 0.2687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8869
moved from start:          0.0970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  16677  Z= 0.116
  Angle     :  0.524   6.887  22572  Z= 0.270
  Chirality :  0.043   0.141   2634
  Planarity :  0.004   0.059   2931
  Dihedral  :  4.051  22.774   2293
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 28.59 %
    Favored  : 68.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.19), residues: 2124
  helix:  2.57 (0.19), residues: 738
  sheet:  0.50 (0.23), residues: 503
  loop : -0.89 (0.23), residues: 883

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 184 
 HIS   0.005   0.001   HIS A 304 
 PHE   0.014   0.001   PHE A 545 
 TYR   0.015   0.001   TYR B 334 
 ARG   0.008   0.000   ARG C 749 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03849 (  888)
  hydrogen bonds       : angle       4.71680 ( 2454)
  covalent geometry    : bond        0.00247 (16677)
  covalent geometry    : angle       0.52448 (22572)

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

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

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 59
  time to evaluate  : 1.875 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 MET cc_start: 0.8482 (tmm) cc_final: 0.8261 (tmm)
REVERT: A  496 MET cc_start: 0.9258 (tpt) cc_final: 0.9048 (tpp)
REVERT: A  543 MET cc_start: 0.8603 (ppp) cc_final: 0.7789 (ppp)
REVERT: B  116 TYR cc_start: 0.7318 (OUTLIER) cc_final: 0.6248 (t80)
REVERT: B  439 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8608 (ttpp)
REVERT: C  104 GLN cc_start: 0.9079 (OUTLIER) cc_final: 0.8544 (tt0)
REVERT: C  209 MET cc_start: 0.9155 (tpp) cc_final: 0.8615 (mpp)
REVERT: C  424 MET cc_start: 0.8426 (tmm) cc_final: 0.8059 (tmm)
REVERT: C  577 GLN cc_start: 0.9512 (OUTLIER) cc_final: 0.9030 (mt0)
REVERT: C  675 GLN cc_start: 0.5668 (OUTLIER) cc_final: 0.5299 (mm110)
  outliers start: 56
  outliers final: 33
  residues processed: 110
  average time/residue: 0.2852
  time to fit residues: 49.0076
Evaluate side-chains
  97 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 59
  time to evaluate  : 1.848 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 MET
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  138 ILE
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  332 ASP
Chi-restraints excluded: chain A residue  367 LEU
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  378 LYS
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  547 ILE
Chi-restraints excluded: chain A residue  631 LEU
Chi-restraints excluded: chain A residue  681 VAL
Chi-restraints excluded: chain A residue  733 VAL
Chi-restraints excluded: chain A residue  744 ARG
Chi-restraints excluded: chain B residue   53 ASN
Chi-restraints excluded: chain B residue   91 SER
Chi-restraints excluded: chain B residue  116 TYR
Chi-restraints excluded: chain B residue  202 VAL
Chi-restraints excluded: chain B residue  324 LEU
Chi-restraints excluded: chain B residue  401 SER
Chi-restraints excluded: chain B residue  423 PHE
Chi-restraints excluded: chain B residue  439 LYS
Chi-restraints excluded: chain B residue  543 MET
Chi-restraints excluded: chain B residue  586 LEU
Chi-restraints excluded: chain B residue  717 ILE
Chi-restraints excluded: chain B residue  738 ARG
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  104 GLN
Chi-restraints excluded: chain C residue  255 ILE
Chi-restraints excluded: chain C residue  272 THR
Chi-restraints excluded: chain C residue  336 ILE
Chi-restraints excluded: chain C residue  397 VAL
Chi-restraints excluded: chain C residue  401 SER
Chi-restraints excluded: chain C residue  498 SER
Chi-restraints excluded: chain C residue  577 GLN
Chi-restraints excluded: chain C residue  612 VAL
Chi-restraints excluded: chain C residue  675 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 114 optimal weight:   10.0000
   chunk 0 optimal weight:    8.9990
   chunk 128 optimal weight:    6.9990
   chunk 59 optimal weight:   10.0000
   chunk 33 optimal weight:   10.0000
   chunk 200 optimal weight:    0.9990
   chunk 113 optimal weight:    2.9990
   chunk 88 optimal weight:    0.7980
   chunk 165 optimal weight:    3.9990
   chunk 6 optimal weight:    0.0670
   chunk 99 optimal weight:    5.9990
   overall best weight:    1.7724

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

Flipped N/Q/H residues before XYZ refinement:
A 627 ASN
** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.064402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.2640 r_free = 0.2640 target = 0.038290 restraints weight = 82392.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 63)----------------|
| r_work = 0.2676 r_free = 0.2676 target = 0.039574 restraints weight = 52820.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2701 r_free = 0.2701 target = 0.040324 restraints weight = 40185.135|
|-----------------------------------------------------------------------------|
r_work (final): 0.2659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8890
moved from start:          0.1027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  16677  Z= 0.155
  Angle     :  0.540   7.827  22572  Z= 0.275
  Chirality :  0.043   0.264   2634
  Planarity :  0.004   0.069   2931
  Dihedral  :  4.020  23.522   2293
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 28.20 %
    Favored  : 68.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.19), residues: 2124
  helix:  2.57 (0.19), residues: 739
  sheet:  0.49 (0.23), residues: 504
  loop : -0.90 (0.23), residues: 881

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP C 184 
 HIS   0.004   0.001   HIS A 304 
 PHE   0.013   0.001   PHE A 545 
 TYR   0.015   0.001   TYR B 334 
 ARG   0.004   0.000   ARG C 119 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03794 (  888)
  hydrogen bonds       : angle       4.64658 ( 2454)
  covalent geometry    : bond        0.00338 (16677)
  covalent geometry    : angle       0.53972 (22572)

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

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

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 59
  time to evaluate  : 2.082 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  228 MET cc_start: 0.8806 (tmm) cc_final: 0.8396 (tmm)
REVERT: A  543 MET cc_start: 0.8679 (ppp) cc_final: 0.7798 (ppp)
REVERT: B  116 TYR cc_start: 0.7467 (OUTLIER) cc_final: 0.6354 (t80)
REVERT: B  123 THR cc_start: 0.8269 (OUTLIER) cc_final: 0.7998 (p)
REVERT: B  228 MET cc_start: 0.8805 (tpp) cc_final: 0.8587 (tpp)
REVERT: B  426 HIS cc_start: 0.8086 (OUTLIER) cc_final: 0.7768 (t-170)
REVERT: B  439 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8651 (ttpp)
REVERT: C  184 TRP cc_start: 0.9144 (OUTLIER) cc_final: 0.8643 (t60)
REVERT: C  424 MET cc_start: 0.8454 (tmm) cc_final: 0.8046 (tmm)
  outliers start: 64
  outliers final: 42
  residues processed: 118
  average time/residue: 0.2500
  time to fit residues: 47.8888
Evaluate side-chains
  105 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 58
  time to evaluate  : 1.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 MET
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  138 ILE
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  310 ASP
Chi-restraints excluded: chain A residue  332 ASP
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  378 LYS
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  547 ILE
Chi-restraints excluded: chain A residue  631 LEU
Chi-restraints excluded: chain A residue  653 THR
Chi-restraints excluded: chain A residue  681 VAL
Chi-restraints excluded: chain A residue  682 TYR
Chi-restraints excluded: chain A residue  733 VAL
Chi-restraints excluded: chain A residue  744 ARG
Chi-restraints excluded: chain B residue   53 ASN
Chi-restraints excluded: chain B residue  116 TYR
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  202 VAL
Chi-restraints excluded: chain B residue  401 SER
Chi-restraints excluded: chain B residue  423 PHE
Chi-restraints excluded: chain B residue  426 HIS
Chi-restraints excluded: chain B residue  439 LYS
Chi-restraints excluded: chain B residue  543 MET
Chi-restraints excluded: chain B residue  547 ILE
Chi-restraints excluded: chain B residue  585 ILE
Chi-restraints excluded: chain B residue  586 LEU
Chi-restraints excluded: chain B residue  653 THR
Chi-restraints excluded: chain B residue  658 HIS
Chi-restraints excluded: chain B residue  681 VAL
Chi-restraints excluded: chain B residue  717 ILE
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  154 CYS
Chi-restraints excluded: chain C residue  184 TRP
Chi-restraints excluded: chain C residue  255 ILE
Chi-restraints excluded: chain C residue  272 THR
Chi-restraints excluded: chain C residue  336 ILE
Chi-restraints excluded: chain C residue  397 VAL
Chi-restraints excluded: chain C residue  401 SER
Chi-restraints excluded: chain C residue  498 SER
Chi-restraints excluded: chain C residue  504 SER
Chi-restraints excluded: chain C residue  646 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 76 optimal weight:    4.9990
   chunk 9 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9990
   chunk 158 optimal weight:    7.9990
   chunk 135 optimal weight:   50.0000
   chunk 26 optimal weight:    2.9990
   chunk 17 optimal weight:    7.9990
   chunk 103 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 118 optimal weight:    1.9990
   chunk 180 optimal weight:    0.7980
   overall best weight:    1.3588

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

Flipped N/Q/H residues before XYZ refinement:
A 658 HIS
** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 708 HIS
C 611 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.064671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2666 r_free = 0.2666 target = 0.039345 restraints weight = 82481.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 66)----------------|
| r_work = 0.2695 r_free = 0.2695 target = 0.040384 restraints weight = 51970.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2722 r_free = 0.2722 target = 0.041096 restraints weight = 39053.227|
|-----------------------------------------------------------------------------|
r_work (final): 0.2687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8868
moved from start:          0.1161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  16677  Z= 0.130
  Angle     :  0.530   8.046  22572  Z= 0.268
  Chirality :  0.043   0.188   2634
  Planarity :  0.004   0.057   2931
  Dihedral  :  3.980  23.079   2293
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 28.97 %
    Favored  : 68.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.19), residues: 2124
  helix:  2.57 (0.19), residues: 739
  sheet:  0.52 (0.23), residues: 504
  loop : -0.88 (0.23), residues: 881

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 184 
 HIS   0.004   0.001   HIS A 304 
 PHE   0.012   0.001   PHE A 545 
 TYR   0.015   0.001   TYR B 334 
 ARG   0.004   0.000   ARG A 749 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03648 (  888)
  hydrogen bonds       : angle       4.55139 ( 2454)
  covalent geometry    : bond        0.00282 (16677)
  covalent geometry    : angle       0.52978 (22572)

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

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

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 59
  time to evaluate  : 1.948 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  228 MET cc_start: 0.8759 (tmm) cc_final: 0.8419 (tmm)
REVERT: A  496 MET cc_start: 0.9284 (tpp) cc_final: 0.8825 (tpp)
REVERT: A  543 MET cc_start: 0.8681 (ppp) cc_final: 0.7782 (ppp)
REVERT: B  116 TYR cc_start: 0.7194 (OUTLIER) cc_final: 0.5910 (t80)
REVERT: B  335 GLU cc_start: 0.9401 (OUTLIER) cc_final: 0.8873 (tp30)
REVERT: B  426 HIS cc_start: 0.8116 (OUTLIER) cc_final: 0.7849 (t-170)
REVERT: B  439 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8668 (ttpp)
REVERT: C  184 TRP cc_start: 0.9123 (OUTLIER) cc_final: 0.8654 (t60)
REVERT: C  424 MET cc_start: 0.8447 (tmm) cc_final: 0.8031 (tmm)
REVERT: C  577 GLN cc_start: 0.9507 (OUTLIER) cc_final: 0.9040 (mt0)
  outliers start: 54
  outliers final: 37
  residues processed: 108
  average time/residue: 0.2335
  time to fit residues: 41.9806
Evaluate side-chains
  101 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 58
  time to evaluate  : 1.820 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 MET
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  138 ILE
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  332 ASP
Chi-restraints excluded: chain A residue  367 LEU
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  378 LYS
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  547 ILE
Chi-restraints excluded: chain A residue  631 LEU
Chi-restraints excluded: chain A residue  681 VAL
Chi-restraints excluded: chain A residue  682 TYR
Chi-restraints excluded: chain A residue  733 VAL
Chi-restraints excluded: chain A residue  744 ARG
Chi-restraints excluded: chain B residue   53 ASN
Chi-restraints excluded: chain B residue  116 TYR
Chi-restraints excluded: chain B residue  202 VAL
Chi-restraints excluded: chain B residue  324 LEU
Chi-restraints excluded: chain B residue  335 GLU
Chi-restraints excluded: chain B residue  401 SER
Chi-restraints excluded: chain B residue  423 PHE
Chi-restraints excluded: chain B residue  426 HIS
Chi-restraints excluded: chain B residue  439 LYS
Chi-restraints excluded: chain B residue  543 MET
Chi-restraints excluded: chain B residue  547 ILE
Chi-restraints excluded: chain B residue  585 ILE
Chi-restraints excluded: chain B residue  586 LEU
Chi-restraints excluded: chain B residue  681 VAL
Chi-restraints excluded: chain B residue  717 ILE
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  154 CYS
Chi-restraints excluded: chain C residue  184 TRP
Chi-restraints excluded: chain C residue  255 ILE
Chi-restraints excluded: chain C residue  272 THR
Chi-restraints excluded: chain C residue  336 ILE
Chi-restraints excluded: chain C residue  397 VAL
Chi-restraints excluded: chain C residue  401 SER
Chi-restraints excluded: chain C residue  498 SER
Chi-restraints excluded: chain C residue  504 SER
Chi-restraints excluded: chain C residue  577 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 154 optimal weight:    3.9990
   chunk 190 optimal weight:    5.9990
   chunk 186 optimal weight:    9.9990
   chunk 19 optimal weight:    6.9990
   chunk 11 optimal weight:    8.9990
   chunk 61 optimal weight:    6.9990
   chunk 43 optimal weight:   10.0000
   chunk 203 optimal weight:    4.9990
   chunk 138 optimal weight:    3.9990
   chunk 167 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 708 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.072177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.045131 restraints weight = 97626.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.046609 restraints weight = 60367.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.047405 restraints weight = 45383.464|
|-----------------------------------------------------------------------------|
r_work (final): 0.2656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8934
moved from start:          0.1121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.082  16677  Z= 0.301
  Angle     :  0.649  10.204  22572  Z= 0.325
  Chirality :  0.043   0.163   2634
  Planarity :  0.004   0.067   2931
  Dihedral  :  4.183  23.711   2293
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.69 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 28.48 %
    Favored  : 67.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.19), residues: 2124
  helix:  2.37 (0.19), residues: 740
  sheet:  0.44 (0.24), residues: 503
  loop : -1.04 (0.22), residues: 881

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 184 
 HIS   0.004   0.001   HIS B 426 
 PHE   0.008   0.001   PHE A 545 
 TYR   0.016   0.001   TYR B 334 
 ARG   0.006   0.001   ARG C 119 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04130 (  888)
  hydrogen bonds       : angle       4.84659 ( 2454)
  covalent geometry    : bond        0.00650 (16677)
  covalent geometry    : angle       0.64897 (22572)

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

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

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 59
  time to evaluate  : 1.818 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 MET cc_start: 0.8558 (tmm) cc_final: 0.8303 (tmm)
REVERT: A  228 MET cc_start: 0.8767 (tmm) cc_final: 0.8414 (tmm)
REVERT: A  496 MET cc_start: 0.9340 (tpp) cc_final: 0.9061 (tpp)
REVERT: A  543 MET cc_start: 0.8680 (ppp) cc_final: 0.7766 (ppp)
REVERT: B   44 MET cc_start: 0.5385 (tpt) cc_final: 0.4861 (mmp)
REVERT: B   49 VAL cc_start: 0.9387 (OUTLIER) cc_final: 0.9151 (p)
REVERT: B  116 TYR cc_start: 0.7314 (OUTLIER) cc_final: 0.7041 (t80)
REVERT: B  184 TRP cc_start: 0.9298 (OUTLIER) cc_final: 0.8461 (t60)
REVERT: C  184 TRP cc_start: 0.9284 (OUTLIER) cc_final: 0.8851 (t60)
REVERT: C  424 MET cc_start: 0.8478 (tmm) cc_final: 0.8019 (tmm)
REVERT: C  577 GLN cc_start: 0.9531 (OUTLIER) cc_final: 0.9053 (mt0)
  outliers start: 76
  outliers final: 58
  residues processed: 128
  average time/residue: 0.2264
  time to fit residues: 48.3768
Evaluate side-chains
  121 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 58
  time to evaluate  : 1.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 MET
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  138 ILE
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  310 ASP
Chi-restraints excluded: chain A residue  332 ASP
Chi-restraints excluded: chain A residue  367 LEU
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  378 LYS
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  503 SER
Chi-restraints excluded: chain A residue  509 VAL
Chi-restraints excluded: chain A residue  547 ILE
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  631 LEU
Chi-restraints excluded: chain A residue  653 THR
Chi-restraints excluded: chain A residue  681 VAL
Chi-restraints excluded: chain A residue  682 TYR
Chi-restraints excluded: chain A residue  733 VAL
Chi-restraints excluded: chain A residue  744 ARG
Chi-restraints excluded: chain B residue   49 VAL
Chi-restraints excluded: chain B residue   53 ASN
Chi-restraints excluded: chain B residue   91 SER
Chi-restraints excluded: chain B residue  116 TYR
Chi-restraints excluded: chain B residue  184 TRP
Chi-restraints excluded: chain B residue  202 VAL
Chi-restraints excluded: chain B residue  324 LEU
Chi-restraints excluded: chain B residue  401 SER
Chi-restraints excluded: chain B residue  423 PHE
Chi-restraints excluded: chain B residue  543 MET
Chi-restraints excluded: chain B residue  547 ILE
Chi-restraints excluded: chain B residue  585 ILE
Chi-restraints excluded: chain B residue  586 LEU
Chi-restraints excluded: chain B residue  593 ILE
Chi-restraints excluded: chain B residue  653 THR
Chi-restraints excluded: chain B residue  681 VAL
Chi-restraints excluded: chain B residue  703 THR
Chi-restraints excluded: chain B residue  717 ILE
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  154 CYS
Chi-restraints excluded: chain C residue  184 TRP
Chi-restraints excluded: chain C residue  213 THR
Chi-restraints excluded: chain C residue  245 ILE
Chi-restraints excluded: chain C residue  255 ILE
Chi-restraints excluded: chain C residue  272 THR
Chi-restraints excluded: chain C residue  336 ILE
Chi-restraints excluded: chain C residue  397 VAL
Chi-restraints excluded: chain C residue  401 SER
Chi-restraints excluded: chain C residue  498 SER
Chi-restraints excluded: chain C residue  504 SER
Chi-restraints excluded: chain C residue  577 GLN
Chi-restraints excluded: chain C residue  585 ILE
Chi-restraints excluded: chain C residue  612 VAL
Chi-restraints excluded: chain C residue  646 THR
Chi-restraints excluded: chain C residue  653 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 104 optimal weight:    3.9990
   chunk 125 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 162 optimal weight:    0.9990
   chunk 99 optimal weight:    2.9990
   chunk 95 optimal weight:    0.6980
   chunk 35 optimal weight:    0.8980
   chunk 201 optimal weight:    0.9990
   chunk 37 optimal weight:    4.9990
   chunk 212 optimal weight:   50.0000
   chunk 57 optimal weight:    1.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 708 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.064595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2658 r_free = 0.2658 target = 0.039238 restraints weight = 81293.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2701 r_free = 0.2701 target = 0.040397 restraints weight = 51765.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 61)----------------|
| r_work = 0.2715 r_free = 0.2715 target = 0.041264 restraints weight = 39140.745|
|-----------------------------------------------------------------------------|
r_work (final): 0.2679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8858
moved from start:          0.1255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  16677  Z= 0.119
  Angle     :  0.548   8.435  22572  Z= 0.276
  Chirality :  0.043   0.141   2634
  Planarity :  0.004   0.062   2931
  Dihedral  :  4.072  24.465   2293
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 29.42 %
    Favored  : 67.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.19), residues: 2124
  helix:  2.61 (0.19), residues: 739
  sheet:  0.49 (0.24), residues: 503
  loop : -0.89 (0.23), residues: 882

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 184 
 HIS   0.005   0.001   HIS A 304 
 PHE   0.013   0.001   PHE A 545 
 TYR   0.014   0.001   TYR A 334 
 ARG   0.004   0.000   ARG A 749 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03725 (  888)
  hydrogen bonds       : angle       4.54276 ( 2454)
  covalent geometry    : bond        0.00257 (16677)
  covalent geometry    : angle       0.54818 (22572)

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

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

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 59
  time to evaluate  : 2.030 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 MET cc_start: 0.8376 (tmm) cc_final: 0.8159 (tmm)
REVERT: A  228 MET cc_start: 0.8740 (tmm) cc_final: 0.8422 (tmm)
REVERT: A  543 MET cc_start: 0.8710 (ppp) cc_final: 0.7781 (ppp)
REVERT: B   44 MET cc_start: 0.5404 (tpt) cc_final: 0.4908 (mmp)
REVERT: B  116 TYR cc_start: 0.7259 (OUTLIER) cc_final: 0.5935 (t80)
REVERT: B  184 TRP cc_start: 0.9128 (OUTLIER) cc_final: 0.8494 (t60)
REVERT: B  335 GLU cc_start: 0.9419 (OUTLIER) cc_final: 0.9111 (tp30)
REVERT: B  426 HIS cc_start: 0.8153 (OUTLIER) cc_final: 0.7817 (t-170)
REVERT: C  184 TRP cc_start: 0.9116 (OUTLIER) cc_final: 0.8617 (t60)
REVERT: C  424 MET cc_start: 0.8466 (tmm) cc_final: 0.8021 (tmm)
REVERT: C  577 GLN cc_start: 0.9519 (OUTLIER) cc_final: 0.9031 (mt0)
  outliers start: 63
  outliers final: 49
  residues processed: 116
  average time/residue: 0.2426
  time to fit residues: 46.8407
Evaluate side-chains
  113 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 58
  time to evaluate  : 2.027 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 MET
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  138 ILE
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  269 THR
Chi-restraints excluded: chain A residue  310 ASP
Chi-restraints excluded: chain A residue  332 ASP
Chi-restraints excluded: chain A residue  367 LEU
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  378 LYS
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  509 VAL
Chi-restraints excluded: chain A residue  547 ILE
Chi-restraints excluded: chain A residue  631 LEU
Chi-restraints excluded: chain A residue  681 VAL
Chi-restraints excluded: chain A residue  682 TYR
Chi-restraints excluded: chain A residue  744 ARG
Chi-restraints excluded: chain B residue   53 ASN
Chi-restraints excluded: chain B residue   91 SER
Chi-restraints excluded: chain B residue  116 TYR
Chi-restraints excluded: chain B residue  184 TRP
Chi-restraints excluded: chain B residue  230 GLU
Chi-restraints excluded: chain B residue  324 LEU
Chi-restraints excluded: chain B residue  335 GLU
Chi-restraints excluded: chain B residue  401 SER
Chi-restraints excluded: chain B residue  423 PHE
Chi-restraints excluded: chain B residue  426 HIS
Chi-restraints excluded: chain B residue  543 MET
Chi-restraints excluded: chain B residue  547 ILE
Chi-restraints excluded: chain B residue  585 ILE
Chi-restraints excluded: chain B residue  586 LEU
Chi-restraints excluded: chain B residue  593 ILE
Chi-restraints excluded: chain B residue  681 VAL
Chi-restraints excluded: chain B residue  703 THR
Chi-restraints excluded: chain B residue  717 ILE
Chi-restraints excluded: chain B residue  721 THR
Chi-restraints excluded: chain C residue   75 SER
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue   86 SER
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  154 CYS
Chi-restraints excluded: chain C residue  184 TRP
Chi-restraints excluded: chain C residue  255 ILE
Chi-restraints excluded: chain C residue  272 THR
Chi-restraints excluded: chain C residue  278 THR
Chi-restraints excluded: chain C residue  336 ILE
Chi-restraints excluded: chain C residue  397 VAL
Chi-restraints excluded: chain C residue  401 SER
Chi-restraints excluded: chain C residue  411 VAL
Chi-restraints excluded: chain C residue  498 SER
Chi-restraints excluded: chain C residue  577 GLN
Chi-restraints excluded: chain C residue  612 VAL
Chi-restraints excluded: chain C residue  646 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 65 optimal weight:    6.9990
   chunk 169 optimal weight:    2.9990
   chunk 193 optimal weight:    5.9990
   chunk 208 optimal weight:    8.9990
   chunk 119 optimal weight:    4.9990
   chunk 191 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 172 optimal weight:    0.9980
   chunk 111 optimal weight:    2.9990
   chunk 198 optimal weight:    2.9990
   chunk 95 optimal weight:    6.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 708 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.063837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.2625 r_free = 0.2625 target = 0.038273 restraints weight = 82598.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 76)----------------|
| r_work = 0.2658 r_free = 0.2658 target = 0.039435 restraints weight = 53364.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2684 r_free = 0.2684 target = 0.040123 restraints weight = 40496.661|
|-----------------------------------------------------------------------------|
r_work (final): 0.2649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8898
moved from start:          0.1236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  16677  Z= 0.191
  Angle     :  0.589  10.845  22572  Z= 0.291
  Chirality :  0.042   0.134   2634
  Planarity :  0.004   0.059   2931
  Dihedral  :  4.076  25.730   2293
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 11.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 29.69 %
    Favored  : 66.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.19), residues: 2124
  helix:  2.58 (0.19), residues: 739
  sheet:  0.49 (0.24), residues: 503
  loop : -0.93 (0.23), residues: 882

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 184 
 HIS   0.003   0.001   HIS A 304 
 PHE   0.009   0.001   PHE A 545 
 TYR   0.015   0.001   TYR B 334 
 ARG   0.005   0.000   ARG C 119 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03793 (  888)
  hydrogen bonds       : angle       4.58890 ( 2454)
  covalent geometry    : bond        0.00417 (16677)
  covalent geometry    : angle       0.58913 (22572)

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

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

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 58
  time to evaluate  : 2.089 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 MET cc_start: 0.8452 (tmm) cc_final: 0.8200 (tmm)
REVERT: A  228 MET cc_start: 0.8758 (tmm) cc_final: 0.8438 (tmm)
REVERT: A  543 MET cc_start: 0.8706 (ppp) cc_final: 0.7788 (ppp)
REVERT: B   44 MET cc_start: 0.5375 (tpt) cc_final: 0.4873 (mmp)
REVERT: B  116 TYR cc_start: 0.7394 (OUTLIER) cc_final: 0.6086 (t80)
REVERT: B  184 TRP cc_start: 0.9193 (OUTLIER) cc_final: 0.8477 (t60)
REVERT: B  209 MET cc_start: 0.9343 (tpp) cc_final: 0.9044 (mpp)
REVERT: B  335 GLU cc_start: 0.9401 (OUTLIER) cc_final: 0.9067 (tp30)
REVERT: C  184 TRP cc_start: 0.9183 (OUTLIER) cc_final: 0.8682 (t60)
REVERT: C  209 MET cc_start: 0.9325 (mmm) cc_final: 0.8802 (mpp)
REVERT: C  424 MET cc_start: 0.8472 (tmm) cc_final: 0.8022 (tmm)
REVERT: C  577 GLN cc_start: 0.9518 (OUTLIER) cc_final: 0.9045 (mt0)
  outliers start: 61
  outliers final: 51
  residues processed: 113
  average time/residue: 0.2377
  time to fit residues: 45.1405
Evaluate side-chains
  114 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 58
  time to evaluate  : 1.845 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 MET
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  138 ILE
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  269 THR
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  310 ASP
Chi-restraints excluded: chain A residue  332 ASP
Chi-restraints excluded: chain A residue  367 LEU
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  378 LYS
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  509 VAL
Chi-restraints excluded: chain A residue  547 ILE
Chi-restraints excluded: chain A residue  631 LEU
Chi-restraints excluded: chain A residue  681 VAL
Chi-restraints excluded: chain A residue  682 TYR
Chi-restraints excluded: chain A residue  733 VAL
Chi-restraints excluded: chain A residue  744 ARG
Chi-restraints excluded: chain B residue   53 ASN
Chi-restraints excluded: chain B residue   91 SER
Chi-restraints excluded: chain B residue  116 TYR
Chi-restraints excluded: chain B residue  184 TRP
Chi-restraints excluded: chain B residue  202 VAL
Chi-restraints excluded: chain B residue  230 GLU
Chi-restraints excluded: chain B residue  324 LEU
Chi-restraints excluded: chain B residue  335 GLU
Chi-restraints excluded: chain B residue  401 SER
Chi-restraints excluded: chain B residue  423 PHE
Chi-restraints excluded: chain B residue  543 MET
Chi-restraints excluded: chain B residue  547 ILE
Chi-restraints excluded: chain B residue  585 ILE
Chi-restraints excluded: chain B residue  586 LEU
Chi-restraints excluded: chain B residue  593 ILE
Chi-restraints excluded: chain B residue  681 VAL
Chi-restraints excluded: chain B residue  703 THR
Chi-restraints excluded: chain B residue  717 ILE
Chi-restraints excluded: chain B residue  721 THR
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue   86 SER
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  154 CYS
Chi-restraints excluded: chain C residue  184 TRP
Chi-restraints excluded: chain C residue  255 ILE
Chi-restraints excluded: chain C residue  272 THR
Chi-restraints excluded: chain C residue  278 THR
Chi-restraints excluded: chain C residue  336 ILE
Chi-restraints excluded: chain C residue  397 VAL
Chi-restraints excluded: chain C residue  401 SER
Chi-restraints excluded: chain C residue  498 SER
Chi-restraints excluded: chain C residue  577 GLN
Chi-restraints excluded: chain C residue  612 VAL
Chi-restraints excluded: chain C residue  646 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 104 optimal weight:    7.9990
   chunk 28 optimal weight:    0.0980
   chunk 91 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9980
   chunk 115 optimal weight:   10.0000
   chunk 101 optimal weight:    0.8980
   chunk 125 optimal weight:    1.9990
   chunk 204 optimal weight:    4.9990
   chunk 170 optimal weight:    6.9990
   chunk 1 optimal weight:    6.9990
   chunk 124 optimal weight:    0.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 708 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.065953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2630 r_free = 0.2630 target = 0.043902 restraints weight = 88588.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2679 r_free = 0.2679 target = 0.045273 restraints weight = 52378.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2712 r_free = 0.2712 target = 0.046294 restraints weight = 37419.441|
|-----------------------------------------------------------------------------|
r_work (final): 0.2721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8688
moved from start:          0.1382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  16677  Z= 0.115
  Angle     :  0.554  10.107  22572  Z= 0.274
  Chirality :  0.043   0.142   2634
  Planarity :  0.004   0.057   2931
  Dihedral  :  4.017  27.997   2293
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 29.97 %
    Favored  : 67.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.19), residues: 2124
  helix:  2.68 (0.19), residues: 733
  sheet:  0.56 (0.24), residues: 504
  loop : -0.88 (0.23), residues: 887

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 184 
 HIS   0.004   0.001   HIS A 304 
 PHE   0.012   0.001   PHE A 545 
 TYR   0.015   0.001   TYR A 334 
 ARG   0.003   0.000   ARG C 749 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03561 (  888)
  hydrogen bonds       : angle       4.42229 ( 2454)
  covalent geometry    : bond        0.00251 (16677)
  covalent geometry    : angle       0.55399 (22572)

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

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

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 59
  time to evaluate  : 1.844 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 MET cc_start: 0.8475 (tmm) cc_final: 0.8252 (tmm)
REVERT: A  543 MET cc_start: 0.8674 (ppp) cc_final: 0.7750 (ppp)
REVERT: B   44 MET cc_start: 0.5348 (tpt) cc_final: 0.4846 (mmp)
REVERT: B  116 TYR cc_start: 0.7230 (OUTLIER) cc_final: 0.5933 (t80)
REVERT: B  335 GLU cc_start: 0.9421 (OUTLIER) cc_final: 0.9105 (tp30)
REVERT: C  184 TRP cc_start: 0.9105 (OUTLIER) cc_final: 0.8604 (t60)
REVERT: C  209 MET cc_start: 0.9354 (mmm) cc_final: 0.8798 (mpp)
REVERT: C  424 MET cc_start: 0.8480 (tmm) cc_final: 0.8022 (tmm)
  outliers start: 55
  outliers final: 49
  residues processed: 107
  average time/residue: 0.2293
  time to fit residues: 41.3131
Evaluate side-chains
  110 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 58
  time to evaluate  : 1.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 MET
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  138 ILE
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  269 THR
Chi-restraints excluded: chain A residue  310 ASP
Chi-restraints excluded: chain A residue  332 ASP
Chi-restraints excluded: chain A residue  367 LEU
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  378 LYS
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  509 VAL
Chi-restraints excluded: chain A residue  547 ILE
Chi-restraints excluded: chain A residue  631 LEU
Chi-restraints excluded: chain A residue  681 VAL
Chi-restraints excluded: chain A residue  682 TYR
Chi-restraints excluded: chain A residue  733 VAL
Chi-restraints excluded: chain A residue  744 ARG
Chi-restraints excluded: chain B residue  116 TYR
Chi-restraints excluded: chain B residue  202 VAL
Chi-restraints excluded: chain B residue  230 GLU
Chi-restraints excluded: chain B residue  324 LEU
Chi-restraints excluded: chain B residue  335 GLU
Chi-restraints excluded: chain B residue  401 SER
Chi-restraints excluded: chain B residue  423 PHE
Chi-restraints excluded: chain B residue  543 MET
Chi-restraints excluded: chain B residue  547 ILE
Chi-restraints excluded: chain B residue  585 ILE
Chi-restraints excluded: chain B residue  586 LEU
Chi-restraints excluded: chain B residue  681 VAL
Chi-restraints excluded: chain B residue  703 THR
Chi-restraints excluded: chain B residue  717 ILE
Chi-restraints excluded: chain B residue  721 THR
Chi-restraints excluded: chain C residue   44 MET
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue   86 SER
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  154 CYS
Chi-restraints excluded: chain C residue  184 TRP
Chi-restraints excluded: chain C residue  213 THR
Chi-restraints excluded: chain C residue  255 ILE
Chi-restraints excluded: chain C residue  272 THR
Chi-restraints excluded: chain C residue  304 HIS
Chi-restraints excluded: chain C residue  336 ILE
Chi-restraints excluded: chain C residue  397 VAL
Chi-restraints excluded: chain C residue  401 SER
Chi-restraints excluded: chain C residue  498 SER
Chi-restraints excluded: chain C residue  612 VAL
Chi-restraints excluded: chain C residue  646 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 4 optimal weight:    0.7980
   chunk 82 optimal weight:    3.9990
   chunk 142 optimal weight:    7.9990
   chunk 79 optimal weight:    0.9990
   chunk 209 optimal weight:    0.9990
   chunk 147 optimal weight:    5.9990
   chunk 164 optimal weight:    0.0870
   chunk 40 optimal weight:    0.9990
   chunk 93 optimal weight:    3.9990
   chunk 158 optimal weight:    0.9990
   chunk 56 optimal weight:    0.4980
   overall best weight:    0.6762

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

Flipped N/Q/H residues before XYZ refinement:
** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.066566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2655 r_free = 0.2655 target = 0.044480 restraints weight = 87779.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2702 r_free = 0.2702 target = 0.045865 restraints weight = 51869.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2736 r_free = 0.2736 target = 0.046867 restraints weight = 36806.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.2747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8667
moved from start:          0.1533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  16677  Z= 0.104
  Angle     :  0.559  10.460  22572  Z= 0.273
  Chirality :  0.043   0.180   2634
  Planarity :  0.003   0.055   2931
  Dihedral  :  3.950  30.017   2293
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 30.19 %
    Favored  : 67.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.19), residues: 2124
  helix:  2.71 (0.19), residues: 734
  sheet:  0.63 (0.24), residues: 505
  loop : -0.84 (0.23), residues: 885

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C 184 
 HIS   0.004   0.001   HIS A 304 
 PHE   0.013   0.001   PHE A 545 
 TYR   0.013   0.001   TYR B 334 
 ARG   0.003   0.000   ARG B 746 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03370 (  888)
  hydrogen bonds       : angle       4.34661 ( 2454)
  covalent geometry    : bond        0.00226 (16677)
  covalent geometry    : angle       0.55871 (22572)

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

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

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4248 Ramachandran restraints generated.
    2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 60
  time to evaluate  : 1.973 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  439 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8339 (ptmm)
REVERT: A  485 MET cc_start: 0.9072 (mmp) cc_final: 0.8795 (mmp)
REVERT: A  543 MET cc_start: 0.8663 (ppp) cc_final: 0.7736 (ppp)
REVERT: B   44 MET cc_start: 0.5352 (tpt) cc_final: 0.4859 (mmp)
REVERT: B  116 TYR cc_start: 0.7219 (OUTLIER) cc_final: 0.5892 (t80)
REVERT: B  335 GLU cc_start: 0.9417 (OUTLIER) cc_final: 0.9103 (tp30)
REVERT: C  209 MET cc_start: 0.9351 (mmm) cc_final: 0.8802 (mpp)
REVERT: C  424 MET cc_start: 0.8473 (tmm) cc_final: 0.8020 (tmm)
  outliers start: 51
  outliers final: 45
  residues processed: 105
  average time/residue: 0.2460
  time to fit residues: 42.9187
Evaluate side-chains
  106 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 58
  time to evaluate  : 1.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 MET
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  138 ILE
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  269 THR
Chi-restraints excluded: chain A residue  310 ASP
Chi-restraints excluded: chain A residue  367 LEU
Chi-restraints excluded: chain A residue  378 LYS
Chi-restraints excluded: chain A residue  439 LYS
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  509 VAL
Chi-restraints excluded: chain A residue  547 ILE
Chi-restraints excluded: chain A residue  631 LEU
Chi-restraints excluded: chain A residue  681 VAL
Chi-restraints excluded: chain A residue  682 TYR
Chi-restraints excluded: chain A residue  733 VAL
Chi-restraints excluded: chain A residue  744 ARG
Chi-restraints excluded: chain B residue  116 TYR
Chi-restraints excluded: chain B residue  335 GLU
Chi-restraints excluded: chain B residue  401 SER
Chi-restraints excluded: chain B residue  423 PHE
Chi-restraints excluded: chain B residue  543 MET
Chi-restraints excluded: chain B residue  547 ILE
Chi-restraints excluded: chain B residue  585 ILE
Chi-restraints excluded: chain B residue  586 LEU
Chi-restraints excluded: chain B residue  681 VAL
Chi-restraints excluded: chain B residue  703 THR
Chi-restraints excluded: chain B residue  717 ILE
Chi-restraints excluded: chain B residue  721 THR
Chi-restraints excluded: chain B residue  733 VAL
Chi-restraints excluded: chain C residue   44 MET
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue   86 SER
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  154 CYS
Chi-restraints excluded: chain C residue  213 THR
Chi-restraints excluded: chain C residue  255 ILE
Chi-restraints excluded: chain C residue  272 THR
Chi-restraints excluded: chain C residue  304 HIS
Chi-restraints excluded: chain C residue  336 ILE
Chi-restraints excluded: chain C residue  397 VAL
Chi-restraints excluded: chain C residue  401 SER
Chi-restraints excluded: chain C residue  498 SER
Chi-restraints excluded: chain C residue  612 VAL
Chi-restraints excluded: chain C residue  646 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 213
   random chunks:
   chunk 105 optimal weight:   10.0000
   chunk 178 optimal weight:    6.9990
   chunk 49 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   chunk 181 optimal weight:   10.0000
   chunk 61 optimal weight:    2.9990
   chunk 48 optimal weight:    6.9990
   chunk 193 optimal weight:    7.9990
   chunk 166 optimal weight:    4.9990
   chunk 54 optimal weight:    0.7980
   chunk 141 optimal weight:   40.0000
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
C 611 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.073235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 83)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.045960 restraints weight = 96689.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.047305 restraints weight = 59403.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.048739 restraints weight = 45830.660|
|-----------------------------------------------------------------------------|
r_work (final): 0.2680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8910
moved from start:          0.1373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067  16677  Z= 0.246
  Angle     :  0.643  13.209  22572  Z= 0.313
  Chirality :  0.043   0.210   2634
  Planarity :  0.004   0.057   2931
  Dihedral  :  4.056  31.584   2293
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 29.80 %
    Favored  : 66.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.19), residues: 2124
  helix:  2.61 (0.19), residues: 733
  sheet:  0.60 (0.24), residues: 503
  loop : -0.94 (0.22), residues: 888

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 184 
 HIS   0.003   0.001   HIS B 426 
 PHE   0.007   0.001   PHE A 377 
 TYR   0.015   0.001   TYR B 334 
 ARG   0.005   0.000   ARG C 119 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03753 (  888)
  hydrogen bonds       : angle       4.58909 ( 2454)
  covalent geometry    : bond        0.00532 (16677)
  covalent geometry    : angle       0.64309 (22572)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5023.50 seconds
wall clock time: 89 minutes 20.44 seconds (5360.44 seconds total)