Starting phenix.real_space_refine
on Thu Mar  5 05:22:20 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6uw8_20919/03_2026/6uw8_20919.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6uw8_20919/03_2026/6uw8_20919.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.02
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6uw8_20919/03_2026/6uw8_20919.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6uw8_20919/03_2026/6uw8_20919.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6uw8_20919/03_2026/6uw8_20919.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6uw8_20919/03_2026/6uw8_20919.map"
  }
  resolution = 4.02
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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     116      5.16       5
     C   12800      2.51       5
     N    3260      2.21       5
     O    3464      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 100 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 19640
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4910
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 602, 4910
          Classifications: {'peptide': 602}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 589}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 4910
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 602, 4910
          Classifications: {'peptide': 602}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 589}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 4910
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 602, 4910
          Classifications: {'peptide': 602}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 589}
          Chain breaks: 3
    Chain: "D"
      Number of atoms: 4910
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 602, 4910
          Classifications: {'peptide': 602}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 589}
          Chain breaks: 3
  Time building chain proxies: 3.94, per 1000 atoms: 0.20
  Number of scatterers: 19640
  At special positions: 0
  Unit cell: (158.4, 157.3, 122.1, 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     116     16.00
     O    3464      8.00
     N    3260      7.00
     C   12800      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: 1.70
  Conformation dependent library (CDL) restraints added in 717.7 milliseconds
  

  4752 Ramachandran restraints generated.
    2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4600

  Finding SS restraints...
    Secondary structure from input PDB file:
      120 helices and 4 sheets defined
      67.3% alpha, 2.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.45
  Creating SS restraints...
    Processing helix  chain 'A' and resid 118 through 130
      removed outlier: 3.580A  pdb=" N   SER A 128 " --> pdb=" O   PHE A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 146
    Processing helix  chain 'A' and resid 154 through 163
    Processing helix  chain 'A' and resid 170 through 178
      removed outlier: 3.603A  pdb=" N   ASN A 178 " --> pdb=" O   LYS A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 197
      removed outlier: 3.528A  pdb=" N   ASN A 197 " --> pdb=" O   PHE A 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 204
    Processing helix  chain 'A' and resid 217 through 225
      removed outlier: 3.721A  pdb=" N   ILE A 221 " --> pdb=" O   THR A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 237
    Processing helix  chain 'A' and resid 264 through 272
    Processing helix  chain 'A' and resid 274 through 283
    Processing helix  chain 'A' and resid 298 through 307
    Processing helix  chain 'A' and resid 315 through 329
      removed outlier: 4.082A  pdb=" N   ARG A 319 " --> pdb=" O   ASP A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 336
      removed outlier: 3.549A  pdb=" N   THR A 336 " --> pdb=" O   GLU A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 352
    Processing helix  chain 'A' and resid 353 through 362
    Processing helix  chain 'A' and resid 402 through 410
    Processing helix  chain 'A' and resid 415 through 421
    Processing helix  chain 'A' and resid 425 through 461
      removed outlier: 3.892A  pdb=" N   PHE A 436 " --> pdb=" O   LYS A 432 " (cutoff:3.500A)
      removed outlier: 6.164A  pdb=" N   LYS A 438 " --> pdb=" O   LYS A 434 " (cutoff:3.500A)
      removed outlier: 5.987A  pdb=" N   HIS A 439 " --> pdb=" O   LYS A 435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 507
      removed outlier: 6.644A  pdb=" N   PHE A 489 " --> pdb=" O   LEU A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 516
      removed outlier: 3.615A  pdb=" N   SER A 515 " --> pdb=" O   ASP A 512 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ILE A 516 " --> pdb=" O   LEU A 513 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 512 through 516'
    Processing helix  chain 'A' and resid 521 through 542
    Processing helix  chain 'A' and resid 546 through 561
      removed outlier: 4.259A  pdb=" N   CYS A 550 " --> pdb=" O   GLU A 546 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   ALA A 554 " --> pdb=" O   CYS A 550 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   TRP A 559 " --> pdb=" O   MET A 555 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   ALA A 560 " --> pdb=" O   ALA A 556 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 562 through 568
      removed outlier: 3.773A  pdb=" N   GLY A 568 " --> pdb=" O   TYR A 565 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 572 through 586
      removed outlier: 4.157A  pdb=" N   MET A 578 " --> pdb=" O   MET A 574 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   ILE A 579 " --> pdb=" O   TYR A 575 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   GLN A 580 " --> pdb=" O   SER A 576 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 586 through 607
      removed outlier: 4.619A  pdb=" N   VAL A 596 " --> pdb=" O   PHE A 592 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   PHE A 597 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 624 through 638
      removed outlier: 3.770A  pdb=" N   VAL A 629 " --> pdb=" O   PHE A 625 " (cutoff:3.500A)
      removed outlier: 4.985A  pdb=" N   LEU A 630 " --> pdb=" O   SER A 626 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 650 through 666
    Processing helix  chain 'A' and resid 668 through 686
      removed outlier: 4.141A  pdb=" N   LYS A 686 " --> pdb=" O   GLU A 682 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 688 through 707
    Processing helix  chain 'A' and resid 738 through 747
    Processing helix  chain 'B' and resid 118 through 130
      removed outlier: 3.580A  pdb=" N   SER B 128 " --> pdb=" O   PHE B 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 131 through 146
    Processing helix  chain 'B' and resid 154 through 163
    Processing helix  chain 'B' and resid 170 through 178
      removed outlier: 3.603A  pdb=" N   ASN B 178 " --> pdb=" O   LYS B 174 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 183 through 197
      removed outlier: 3.528A  pdb=" N   ASN B 197 " --> pdb=" O   PHE B 193 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 199 through 204
    Processing helix  chain 'B' and resid 217 through 225
      removed outlier: 3.721A  pdb=" N   ILE B 221 " --> pdb=" O   THR B 217 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 227 through 237
    Processing helix  chain 'B' and resid 264 through 272
    Processing helix  chain 'B' and resid 274 through 283
    Processing helix  chain 'B' and resid 298 through 307
    Processing helix  chain 'B' and resid 315 through 329
      removed outlier: 4.083A  pdb=" N   ARG B 319 " --> pdb=" O   ASP B 315 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 331 through 336
      removed outlier: 3.548A  pdb=" N   THR B 336 " --> pdb=" O   GLU B 332 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 343 through 352
    Processing helix  chain 'B' and resid 353 through 362
    Processing helix  chain 'B' and resid 402 through 410
    Processing helix  chain 'B' and resid 415 through 421
    Processing helix  chain 'B' and resid 425 through 461
      removed outlier: 3.893A  pdb=" N   PHE B 436 " --> pdb=" O   LYS B 432 " (cutoff:3.500A)
      removed outlier: 6.164A  pdb=" N   LYS B 438 " --> pdb=" O   LYS B 434 " (cutoff:3.500A)
      removed outlier: 5.987A  pdb=" N   HIS B 439 " --> pdb=" O   LYS B 435 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 483 through 507
      removed outlier: 6.643A  pdb=" N   PHE B 489 " --> pdb=" O   LEU B 485 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 512 through 516
      removed outlier: 3.616A  pdb=" N   SER B 515 " --> pdb=" O   ASP B 512 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ILE B 516 " --> pdb=" O   LEU B 513 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 512 through 516'
    Processing helix  chain 'B' and resid 521 through 542
    Processing helix  chain 'B' and resid 546 through 561
      removed outlier: 4.259A  pdb=" N   CYS B 550 " --> pdb=" O   GLU B 546 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   ALA B 554 " --> pdb=" O   CYS B 550 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   TRP B 559 " --> pdb=" O   MET B 555 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   ALA B 560 " --> pdb=" O   ALA B 556 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 562 through 568
      removed outlier: 3.773A  pdb=" N   GLY B 568 " --> pdb=" O   TYR B 565 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 572 through 586
      removed outlier: 4.157A  pdb=" N   MET B 578 " --> pdb=" O   MET B 574 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   ILE B 579 " --> pdb=" O   TYR B 575 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   GLN B 580 " --> pdb=" O   SER B 576 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 586 through 607
      removed outlier: 4.619A  pdb=" N   VAL B 596 " --> pdb=" O   PHE B 592 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   PHE B 597 " --> pdb=" O   VAL B 593 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 624 through 638
      removed outlier: 3.770A  pdb=" N   VAL B 629 " --> pdb=" O   PHE B 625 " (cutoff:3.500A)
      removed outlier: 4.945A  pdb=" N   LEU B 630 " --> pdb=" O   SER B 626 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 650 through 666
    Processing helix  chain 'B' and resid 668 through 686
      removed outlier: 4.141A  pdb=" N   LYS B 686 " --> pdb=" O   GLU B 682 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 688 through 707
    Processing helix  chain 'B' and resid 738 through 747
    Processing helix  chain 'C' and resid 118 through 130
      removed outlier: 3.580A  pdb=" N   SER C 128 " --> pdb=" O   PHE C 124 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 131 through 146
    Processing helix  chain 'C' and resid 154 through 163
    Processing helix  chain 'C' and resid 170 through 178
      removed outlier: 3.603A  pdb=" N   ASN C 178 " --> pdb=" O   LYS C 174 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 183 through 197
      removed outlier: 3.527A  pdb=" N   ASN C 197 " --> pdb=" O   PHE C 193 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 199 through 204
    Processing helix  chain 'C' and resid 217 through 225
      removed outlier: 3.721A  pdb=" N   ILE C 221 " --> pdb=" O   THR C 217 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 227 through 237
    Processing helix  chain 'C' and resid 264 through 272
    Processing helix  chain 'C' and resid 274 through 283
    Processing helix  chain 'C' and resid 298 through 307
    Processing helix  chain 'C' and resid 315 through 329
      removed outlier: 4.082A  pdb=" N   ARG C 319 " --> pdb=" O   ASP C 315 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 331 through 336
      removed outlier: 3.549A  pdb=" N   THR C 336 " --> pdb=" O   GLU C 332 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 343 through 352
    Processing helix  chain 'C' and resid 353 through 362
    Processing helix  chain 'C' and resid 402 through 410
    Processing helix  chain 'C' and resid 415 through 421
    Processing helix  chain 'C' and resid 425 through 461
      removed outlier: 3.892A  pdb=" N   PHE C 436 " --> pdb=" O   LYS C 432 " (cutoff:3.500A)
      removed outlier: 6.164A  pdb=" N   LYS C 438 " --> pdb=" O   LYS C 434 " (cutoff:3.500A)
      removed outlier: 5.988A  pdb=" N   HIS C 439 " --> pdb=" O   LYS C 435 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 483 through 507
      removed outlier: 6.644A  pdb=" N   PHE C 489 " --> pdb=" O   LEU C 485 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 512 through 516
      removed outlier: 3.615A  pdb=" N   SER C 515 " --> pdb=" O   ASP C 512 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   ILE C 516 " --> pdb=" O   LEU C 513 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 512 through 516'
    Processing helix  chain 'C' and resid 521 through 542
    Processing helix  chain 'C' and resid 546 through 561
      removed outlier: 4.258A  pdb=" N   CYS C 550 " --> pdb=" O   GLU C 546 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   ALA C 554 " --> pdb=" O   CYS C 550 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   TRP C 559 " --> pdb=" O   MET C 555 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   ALA C 560 " --> pdb=" O   ALA C 556 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 562 through 568
      removed outlier: 3.773A  pdb=" N   GLY C 568 " --> pdb=" O   TYR C 565 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 572 through 586
      removed outlier: 4.158A  pdb=" N   MET C 578 " --> pdb=" O   MET C 574 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   ILE C 579 " --> pdb=" O   TYR C 575 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   GLN C 580 " --> pdb=" O   SER C 576 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 586 through 607
      removed outlier: 4.619A  pdb=" N   VAL C 596 " --> pdb=" O   PHE C 592 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   PHE C 597 " --> pdb=" O   VAL C 593 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 624 through 638
      removed outlier: 3.770A  pdb=" N   VAL C 629 " --> pdb=" O   PHE C 625 " (cutoff:3.500A)
      removed outlier: 4.965A  pdb=" N   LEU C 630 " --> pdb=" O   SER C 626 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 650 through 666
    Processing helix  chain 'C' and resid 668 through 686
      removed outlier: 4.141A  pdb=" N   LYS C 686 " --> pdb=" O   GLU C 682 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 688 through 707
    Processing helix  chain 'C' and resid 738 through 747
    Processing helix  chain 'D' and resid 118 through 130
      removed outlier: 3.580A  pdb=" N   SER D 128 " --> pdb=" O   PHE D 124 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 131 through 146
    Processing helix  chain 'D' and resid 154 through 163
    Processing helix  chain 'D' and resid 170 through 178
      removed outlier: 3.603A  pdb=" N   ASN D 178 " --> pdb=" O   LYS D 174 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 183 through 197
      removed outlier: 3.528A  pdb=" N   ASN D 197 " --> pdb=" O   PHE D 193 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 199 through 204
    Processing helix  chain 'D' and resid 217 through 225
      removed outlier: 3.721A  pdb=" N   ILE D 221 " --> pdb=" O   THR D 217 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 227 through 237
    Processing helix  chain 'D' and resid 264 through 272
    Processing helix  chain 'D' and resid 274 through 283
    Processing helix  chain 'D' and resid 298 through 307
    Processing helix  chain 'D' and resid 315 through 329
      removed outlier: 4.083A  pdb=" N   ARG D 319 " --> pdb=" O   ASP D 315 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 331 through 336
      removed outlier: 3.549A  pdb=" N   THR D 336 " --> pdb=" O   GLU D 332 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 343 through 352
    Processing helix  chain 'D' and resid 353 through 362
    Processing helix  chain 'D' and resid 402 through 410
    Processing helix  chain 'D' and resid 415 through 421
    Processing helix  chain 'D' and resid 425 through 461
      removed outlier: 3.893A  pdb=" N   PHE D 436 " --> pdb=" O   LYS D 432 " (cutoff:3.500A)
      removed outlier: 6.164A  pdb=" N   LYS D 438 " --> pdb=" O   LYS D 434 " (cutoff:3.500A)
      removed outlier: 5.987A  pdb=" N   HIS D 439 " --> pdb=" O   LYS D 435 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 483 through 507
      removed outlier: 6.644A  pdb=" N   PHE D 489 " --> pdb=" O   LEU D 485 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 512 through 516
      removed outlier: 3.615A  pdb=" N   SER D 515 " --> pdb=" O   ASP D 512 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ILE D 516 " --> pdb=" O   LEU D 513 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 512 through 516'
    Processing helix  chain 'D' and resid 521 through 542
    Processing helix  chain 'D' and resid 546 through 561
      removed outlier: 4.259A  pdb=" N   CYS D 550 " --> pdb=" O   GLU D 546 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   ALA D 554 " --> pdb=" O   CYS D 550 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   TRP D 559 " --> pdb=" O   MET D 555 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   ALA D 560 " --> pdb=" O   ALA D 556 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 562 through 568
      removed outlier: 3.773A  pdb=" N   GLY D 568 " --> pdb=" O   TYR D 565 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 572 through 586
      removed outlier: 4.158A  pdb=" N   MET D 578 " --> pdb=" O   MET D 574 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   ILE D 579 " --> pdb=" O   TYR D 575 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   GLN D 580 " --> pdb=" O   SER D 576 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 586 through 607
      removed outlier: 4.619A  pdb=" N   VAL D 596 " --> pdb=" O   PHE D 592 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   PHE D 597 " --> pdb=" O   VAL D 593 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 624 through 638
      removed outlier: 3.770A  pdb=" N   VAL D 629 " --> pdb=" O   PHE D 625 " (cutoff:3.500A)
      removed outlier: 4.948A  pdb=" N   LEU D 630 " --> pdb=" O   SER D 626 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 650 through 666
    Processing helix  chain 'D' and resid 668 through 686
      removed outlier: 4.141A  pdb=" N   LYS D 686 " --> pdb=" O   GLU D 682 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 688 through 707
    Processing helix  chain 'D' and resid 738 through 747
    Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 382
      removed outlier: 5.267A  pdb=" N   THR A 378 " --> pdb=" O   LEU A 389 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   LEU A 389 " --> pdb=" O   THR A 378 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   TRP A 380 " --> pdb=" O   SER A 387 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 376 through 382
      removed outlier: 5.268A  pdb=" N   THR B 378 " --> pdb=" O   LEU B 389 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   LEU B 389 " --> pdb=" O   THR B 378 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   TRP B 380 " --> pdb=" O   SER B 387 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 376 through 382
      removed outlier: 5.267A  pdb=" N   THR C 378 " --> pdb=" O   LEU C 389 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   LEU C 389 " --> pdb=" O   THR C 378 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   TRP C 380 " --> pdb=" O   SER C 387 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 376 through 382
      removed outlier: 5.267A  pdb=" N   THR D 378 " --> pdb=" O   LEU D 389 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   LEU D 389 " --> pdb=" O   THR D 378 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   TRP D 380 " --> pdb=" O   SER D 387 " (cutoff:3.500A)

    1084 hydrogen bonds defined for protein.
    3192 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.64

  Time building geometry restraints manager: 2.26 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: 6154
        1.34 -     1.46: 4591
        1.46 -     1.58: 9115
        1.58 -     1.70: 4
        1.70 -     1.82: 196
  Bond restraints: 20060
  Sorted by residual:
  bond pdb=" CA  ARG C 118 "
       pdb=" C   ARG C 118 "
    ideal  model  delta    sigma   weight residual
    1.524  1.601 -0.077 1.16e-02 7.43e+03 4.43e+01
  bond pdb=" CA  ARG B 118 "
       pdb=" C   ARG B 118 "
    ideal  model  delta    sigma   weight residual
    1.524  1.600 -0.076 1.16e-02 7.43e+03 4.29e+01
  bond pdb=" CA  ARG A 118 "
       pdb=" C   ARG A 118 "
    ideal  model  delta    sigma   weight residual
    1.524  1.590 -0.066 1.16e-02 7.43e+03 3.25e+01
  bond pdb=" CA  ARG D 118 "
       pdb=" C   ARG D 118 "
    ideal  model  delta    sigma   weight residual
    1.524  1.590 -0.066 1.16e-02 7.43e+03 3.24e+01
  bond pdb=" C   VAL A 154 "
       pdb=" N   PRO A 155 "
    ideal  model  delta    sigma   weight residual
    1.336  1.391 -0.055 1.20e-02 6.94e+03 2.07e+01
  ... (remaining 20055 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.24: 26338
        2.24 -     4.47: 616
        4.47 -     6.71: 129
        6.71 -     8.94: 29
        8.94 -    11.18: 8
  Bond angle restraints: 27120
  Sorted by residual:
  angle pdb=" N   LEU B 119 "
        pdb=" CA  LEU B 119 "
        pdb=" C   LEU B 119 "
      ideal   model   delta    sigma   weight residual
     111.71  122.89  -11.18 1.15e+00 7.56e-01 9.45e+01
  angle pdb=" N   LEU C 119 "
        pdb=" CA  LEU C 119 "
        pdb=" C   LEU C 119 "
      ideal   model   delta    sigma   weight residual
     111.71  122.85  -11.14 1.15e+00 7.56e-01 9.38e+01
  angle pdb=" N   LEU A 119 "
        pdb=" CA  LEU A 119 "
        pdb=" C   LEU A 119 "
      ideal   model   delta    sigma   weight residual
     111.71  122.08  -10.37 1.15e+00 7.56e-01 8.13e+01
  angle pdb=" N   LEU D 119 "
        pdb=" CA  LEU D 119 "
        pdb=" C   LEU D 119 "
      ideal   model   delta    sigma   weight residual
     111.71  122.07  -10.36 1.15e+00 7.56e-01 8.11e+01
  angle pdb=" N   ARG C 118 "
        pdb=" CA  ARG C 118 "
        pdb=" C   ARG C 118 "
      ideal   model   delta    sigma   weight residual
     112.68  121.04   -8.36 1.33e+00 5.65e-01 3.95e+01
  ... (remaining 27115 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.20: 10166
       15.20 -    30.39: 1294
       30.39 -    45.59: 388
       45.59 -    60.78: 44
       60.78 -    75.98: 24
  Dihedral angle restraints: 11916
    sinusoidal: 4832
      harmonic: 7084
  Sorted by residual:
  dihedral pdb=" C   ARG B 118 "
           pdb=" N   ARG B 118 "
           pdb=" CA  ARG B 118 "
           pdb=" CB  ARG B 118 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.59   11.99     0      2.50e+00 1.60e-01 2.30e+01
  dihedral pdb=" C   ARG C 118 "
           pdb=" N   ARG C 118 "
           pdb=" CA  ARG C 118 "
           pdb=" CB  ARG C 118 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.58   11.98     0      2.50e+00 1.60e-01 2.30e+01
  dihedral pdb=" CA  GLU B 687 "
           pdb=" C   GLU B 687 "
           pdb=" N   SER B 688 "
           pdb=" CA  SER B 688 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.06  -21.94     0      5.00e+00 4.00e-02 1.93e+01
  ... (remaining 11913 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.086: 2820
       0.086 -    0.172: 259
       0.172 -    0.257: 13
       0.257 -    0.343: 4
       0.343 -    0.429: 4
  Chirality restraints: 3100
  Sorted by residual:
  chirality pdb=" CA  ARG B 118 "
            pdb=" N   ARG B 118 "
            pdb=" C   ARG B 118 "
            pdb=" CB  ARG B 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.08    0.43 2.00e-01 2.50e+01 4.60e+00
  chirality pdb=" CA  ARG C 118 "
            pdb=" N   ARG C 118 "
            pdb=" C   ARG C 118 "
            pdb=" CB  ARG C 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.08    0.43 2.00e-01 2.50e+01 4.56e+00
  chirality pdb=" CA  ARG A 118 "
            pdb=" N   ARG A 118 "
            pdb=" C   ARG A 118 "
            pdb=" CB  ARG A 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.46e+00
  ... (remaining 3097 not shown)

  Planarity restraints: 3360
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG C 118 "    0.013 2.00e-02 2.50e+03   2.63e-02 6.93e+00
        pdb=" C   ARG C 118 "   -0.045 2.00e-02 2.50e+03
        pdb=" O   ARG C 118 "    0.018 2.00e-02 2.50e+03
        pdb=" N   LEU C 119 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 118 "    0.013 2.00e-02 2.50e+03   2.62e-02 6.88e+00
        pdb=" C   ARG B 118 "   -0.045 2.00e-02 2.50e+03
        pdb=" O   ARG B 118 "    0.018 2.00e-02 2.50e+03
        pdb=" N   LEU B 119 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 118 "    0.011 2.00e-02 2.50e+03   2.36e-02 5.56e+00
        pdb=" C   ARG A 118 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   ARG A 118 "    0.016 2.00e-02 2.50e+03
        pdb=" N   LEU A 119 "    0.013 2.00e-02 2.50e+03
  ... (remaining 3357 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 802
        2.72 -     3.26: 19047
        3.26 -     3.81: 30996
        3.81 -     4.35: 36239
        4.35 -     4.90: 61846
  Nonbonded interactions: 148930
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG B 117 "
            pdb=" NH1 ARG B 118 "
     model   vdw
     2.173 3.200
  nonbonded pdb=" NH2 ARG C 117 "
            pdb=" NH1 ARG C 118 "
     model   vdw
     2.175 3.200
  nonbonded pdb=" NH2 ARG D 117 "
            pdb=" NH1 ARG D 118 "
     model   vdw
     2.203 3.200
  nonbonded pdb=" NH2 ARG A 117 "
            pdb=" NH1 ARG A 118 "
     model   vdw
     2.207 3.200
  nonbonded pdb=" O   LEU C 268 "
            pdb=" OG1 THR C 272 "
     model   vdw
     2.286 3.040
  ... (remaining 148925 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.430
  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:             0.020
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.070
  Set scattering table:                    0.050
  Process input model:                     15.860
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
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   0.083  20060  Z= 0.245
  Angle     :  0.900  11.178  27120  Z= 0.522
  Chirality :  0.053   0.429   3100
  Planarity :  0.006   0.059   3360
  Dihedral  : 14.813  75.977   7316
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.94 %
    Favored  : 92.06 %
  Cbeta Deviations :  0.17 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.15 (0.13), residues: 2376
  helix: -2.28 (0.09), residues: 1576
  sheet: -4.05 (0.39), residues: 76
  loop : -3.29 (0.19), residues: 724

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 693 
 TYR   0.015   0.001   TYR D 594 
 PHE   0.014   0.001   PHE A 377 
 TRP   0.016   0.001   TRP B 433 
 HIS   0.004   0.001   HIS D 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00489 (20060)
  covalent geometry    : angle       0.90015 (27120)
  hydrogen bonds       : bond        0.09187 ( 1084)
  hydrogen bonds       : angle       4.88091 ( 3192)

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

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

  4752 Ramachandran restraints generated.
    2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4752 Ramachandran restraints generated.
    2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  368 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 368
  time to evaluate  : 0.612 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 ARG cc_start: 0.8647 (ttm110) cc_final: 0.8065 (ttm110)
REVERT: A  173 MET cc_start: 0.8845 (mtt) cc_final: 0.8595 (mtt)
REVERT: A  255 GLN cc_start: 0.8437 (tm-30) cc_final: 0.7993 (tt0)
REVERT: A  501 GLU cc_start: 0.8473 (mm-30) cc_final: 0.7981 (mm-30)
REVERT: A  521 TRP cc_start: 0.7785 (t-100) cc_final: 0.7570 (t60)
REVERT: A  553 LEU cc_start: 0.9369 (mt) cc_final: 0.9094 (mt)
REVERT: A  561 ASN cc_start: 0.8879 (m-40) cc_final: 0.8661 (t0)
REVERT: A  574 MET cc_start: 0.7923 (mtt) cc_final: 0.7622 (mtt)
REVERT: B  173 MET cc_start: 0.8715 (mtt) cc_final: 0.8361 (mtt)
REVERT: B  255 GLN cc_start: 0.8375 (tm-30) cc_final: 0.7933 (tt0)
REVERT: B  553 LEU cc_start: 0.9392 (mt) cc_final: 0.9117 (mt)
REVERT: B  562 MET cc_start: 0.9022 (mmm) cc_final: 0.8784 (tpp)
REVERT: C  143 GLN cc_start: 0.8757 (tp-100) cc_final: 0.8464 (pt0)
REVERT: C  255 GLN cc_start: 0.8390 (tm-30) cc_final: 0.7999 (tt0)
REVERT: C  371 ARG cc_start: 0.7044 (tmt170) cc_final: 0.6700 (tpt-90)
REVERT: C  431 MET cc_start: 0.8892 (ttm) cc_final: 0.8637 (mtm)
REVERT: C  501 GLU cc_start: 0.8538 (mm-30) cc_final: 0.7955 (mm-30)
REVERT: C  521 TRP cc_start: 0.7880 (t-100) cc_final: 0.7651 (t60)
REVERT: C  553 LEU cc_start: 0.9387 (mt) cc_final: 0.9117 (mt)
REVERT: C  561 ASN cc_start: 0.8921 (m-40) cc_final: 0.8629 (t0)
REVERT: C  677 MET cc_start: 0.7567 (mtp) cc_final: 0.7336 (mtm)
REVERT: D  122 ARG cc_start: 0.8569 (ttm110) cc_final: 0.7983 (ttm110)
REVERT: D  143 GLN cc_start: 0.8833 (tp-100) cc_final: 0.8632 (mm-40)
REVERT: D  173 MET cc_start: 0.8833 (mtt) cc_final: 0.8576 (mtt)
REVERT: D  255 GLN cc_start: 0.8479 (tm-30) cc_final: 0.7897 (tt0)
REVERT: D  320 MET cc_start: 0.9031 (tpp) cc_final: 0.8804 (tpp)
REVERT: D  553 LEU cc_start: 0.9376 (mt) cc_final: 0.9131 (mt)
REVERT: D  561 ASN cc_start: 0.8887 (m-40) cc_final: 0.8680 (m-40)
REVERT: D  562 MET cc_start: 0.8991 (mmm) cc_final: 0.8603 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 368
  average time/residue: 0.1419
  time to fit residues: 78.7989
Evaluate side-chains
  233 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 233
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 240
   random chunks:
   chunk 216 optimal weight:    1.9990
   chunk 98 optimal weight:    6.9990
   chunk 194 optimal weight:    8.9990
   chunk 227 optimal weight:    5.9990
   chunk 107 optimal weight:    0.2980
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:    8.9990
   chunk 130 optimal weight:    0.0770
   chunk 124 optimal weight:    6.9990
   chunk 103 optimal weight:    3.9990
   chunk 235 optimal weight:    1.9990
   overall best weight:    1.0542

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

Flipped N/Q/H residues before XYZ refinement:
A 242 ASN
** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 339 ASN
A 585 HIS
A 646 GLN
B 242 ASN
** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 339 ASN
B 585 HIS
B 646 GLN
C 143 GLN
C 242 ASN
** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 339 ASN
C 585 HIS
C 646 GLN
D 143 GLN
D 242 ASN
** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 339 ASN
D 585 HIS

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.114990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.090012 restraints weight = 40151.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.092039 restraints weight = 27135.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.093405 restraints weight = 20761.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.094271 restraints weight = 17310.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.095017 restraints weight = 15352.279|
|-----------------------------------------------------------------------------|
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.1771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  20060  Z= 0.108
  Angle     :  0.515   7.407  27120  Z= 0.272
  Chirality :  0.036   0.135   3100
  Planarity :  0.004   0.057   3360
  Dihedral  :  4.569  18.356   2620
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  3.24 %
    Favored  : 96.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.92 (0.16), residues: 2376
  helix: -0.48 (0.12), residues: 1604
  sheet: -2.78 (0.54), residues: 68
  loop : -2.81 (0.21), residues: 704

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 416 
 TYR   0.012   0.001   TYR B 650 
 PHE   0.008   0.001   PHE D 601 
 TRP   0.013   0.001   TRP C 433 
 HIS   0.005   0.000   HIS B 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 (20060)
  covalent geometry    : angle       0.51486 (27120)
  hydrogen bonds       : bond        0.03240 ( 1084)
  hydrogen bonds       : angle       3.73738 ( 3192)

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

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

  4752 Ramachandran restraints generated.
    2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4752 Ramachandran restraints generated.
    2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  341 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 340
  time to evaluate  : 0.704 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 ARG cc_start: 0.8705 (ttm110) cc_final: 0.7793 (ttm110)
REVERT: A  142 LEU cc_start: 0.8463 (tp) cc_final: 0.7681 (tp)
REVERT: A  173 MET cc_start: 0.8820 (mtt) cc_final: 0.8518 (mtt)
REVERT: A  255 GLN cc_start: 0.8309 (tm-30) cc_final: 0.7949 (tt0)
REVERT: A  278 VAL cc_start: 0.9336 (t) cc_final: 0.9075 (t)
REVERT: A  308 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7368 (tm-30)
REVERT: A  320 MET cc_start: 0.9087 (tpp) cc_final: 0.8871 (tpp)
REVERT: A  419 MET cc_start: 0.9096 (mtp) cc_final: 0.8808 (mtp)
REVERT: A  501 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7775 (mm-30)
REVERT: A  561 ASN cc_start: 0.9141 (m-40) cc_final: 0.8817 (t0)
REVERT: A  574 MET cc_start: 0.7827 (mtt) cc_final: 0.7549 (mtt)
REVERT: B  122 ARG cc_start: 0.8759 (ttm110) cc_final: 0.8091 (ttm110)
REVERT: B  308 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7509 (tm-30)
REVERT: B  562 MET cc_start: 0.9027 (mmm) cc_final: 0.8657 (tpp)
REVERT: C  122 ARG cc_start: 0.8693 (ttm110) cc_final: 0.7987 (ttm110)
REVERT: C  255 GLN cc_start: 0.8236 (tm-30) cc_final: 0.7928 (tt0)
REVERT: C  306 VAL cc_start: 0.9291 (t) cc_final: 0.8639 (t)
REVERT: C  308 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7296 (tm-30)
REVERT: C  419 MET cc_start: 0.9057 (mtp) cc_final: 0.8773 (mtp)
REVERT: C  431 MET cc_start: 0.8859 (ttm) cc_final: 0.8627 (mtm)
REVERT: C  501 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7900 (mm-30)
REVERT: C  561 ASN cc_start: 0.9133 (m-40) cc_final: 0.8785 (t0)
REVERT: D  122 ARG cc_start: 0.8701 (ttm110) cc_final: 0.8074 (ttm110)
REVERT: D  159 MET cc_start: 0.7519 (mmm) cc_final: 0.6966 (mmp)
REVERT: D  173 MET cc_start: 0.8818 (mtt) cc_final: 0.8515 (mtt)
REVERT: D  255 GLN cc_start: 0.8344 (tm-30) cc_final: 0.7835 (tt0)
REVERT: D  278 VAL cc_start: 0.9283 (t) cc_final: 0.9011 (t)
REVERT: D  308 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7538 (tm-30)
REVERT: D  320 MET cc_start: 0.8998 (tpp) cc_final: 0.8789 (tpp)
REVERT: D  561 ASN cc_start: 0.9116 (m-40) cc_final: 0.8843 (t0)
REVERT: D  562 MET cc_start: 0.9030 (mmm) cc_final: 0.8673 (tpp)
  outliers start: 1
  outliers final: 0
  residues processed: 340
  average time/residue: 0.1028
  time to fit residues: 57.8924
Evaluate side-chains
  225 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 225
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 240
   random chunks:
   chunk 130 optimal weight:    2.9990
   chunk 85 optimal weight:    4.9990
   chunk 45 optimal weight:    4.9990
   chunk 168 optimal weight:    8.9990
   chunk 79 optimal weight:    2.9990
   chunk 148 optimal weight:    0.9980
   chunk 226 optimal weight:    1.9990
   chunk 164 optimal weight:    5.9990
   chunk 116 optimal weight:    0.9980
   chunk 225 optimal weight:    0.8980
   chunk 155 optimal weight:    0.9980
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 430 HIS
B 430 HIS
C 430 HIS
D 143 GLN
D 197 ASN
** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 430 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.114978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.091332 restraints weight = 40329.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.092971 restraints weight = 28983.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.093983 restraints weight = 23080.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.094854 restraints weight = 19856.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.095363 restraints weight = 17873.451|
|-----------------------------------------------------------------------------|
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.2164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045  20060  Z= 0.108
  Angle     :  0.504   6.959  27120  Z= 0.261
  Chirality :  0.037   0.137   3100
  Planarity :  0.004   0.058   3360
  Dihedral  :  4.178  17.702   2620
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  2.82 %
    Favored  : 97.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.92 (0.17), residues: 2376
  helix:  0.31 (0.13), residues: 1600
  sheet: -2.20 (0.63), residues: 68
  loop : -2.52 (0.22), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 716 
 TYR   0.012   0.001   TYR D 359 
 PHE   0.012   0.001   PHE A 506 
 TRP   0.013   0.001   TRP B 433 
 HIS   0.002   0.001   HIS D 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 (20060)
  covalent geometry    : angle       0.50393 (27120)
  hydrogen bonds       : bond        0.03161 ( 1084)
  hydrogen bonds       : angle       3.61165 ( 3192)

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

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

  4752 Ramachandran restraints generated.
    2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4752 Ramachandran restraints generated.
    2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  350 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 349
  time to evaluate  : 0.717 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 ARG cc_start: 0.8762 (ttm110) cc_final: 0.7814 (ttm110)
REVERT: A  173 MET cc_start: 0.8796 (mtt) cc_final: 0.8526 (mtt)
REVERT: A  255 GLN cc_start: 0.8345 (tm-30) cc_final: 0.7905 (tt0)
REVERT: A  308 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7223 (tm-30)
REVERT: A  419 MET cc_start: 0.9099 (mtp) cc_final: 0.8772 (mtp)
REVERT: A  495 MET cc_start: 0.8385 (mtt) cc_final: 0.8066 (mtp)
REVERT: A  501 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7956 (mm-30)
REVERT: A  561 ASN cc_start: 0.9116 (m-40) cc_final: 0.8817 (t0)
REVERT: A  562 MET cc_start: 0.9005 (mmm) cc_final: 0.8799 (tpp)
REVERT: A  589 LYS cc_start: 0.8574 (ttmt) cc_final: 0.8208 (mmtt)
REVERT: A  635 LEU cc_start: 0.9254 (tp) cc_final: 0.8904 (tt)
REVERT: A  665 THR cc_start: 0.9580 (p) cc_final: 0.9369 (m)
REVERT: B  122 ARG cc_start: 0.8727 (ttm110) cc_final: 0.8041 (ttm110)
REVERT: B  411 THR cc_start: 0.8538 (p) cc_final: 0.8334 (p)
REVERT: B  589 LYS cc_start: 0.8496 (ttmt) cc_final: 0.8272 (mmtt)
REVERT: B  661 TYR cc_start: 0.9114 (t80) cc_final: 0.8060 (t80)
REVERT: C  122 ARG cc_start: 0.8662 (ttm110) cc_final: 0.7923 (ttm110)
REVERT: C  255 GLN cc_start: 0.8315 (tm-30) cc_final: 0.7921 (tt0)
REVERT: C  308 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7193 (tm-30)
REVERT: C  419 MET cc_start: 0.9116 (mtp) cc_final: 0.8820 (mtp)
REVERT: C  495 MET cc_start: 0.8358 (mtt) cc_final: 0.8023 (mtp)
REVERT: C  501 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8014 (mm-30)
REVERT: C  506 PHE cc_start: 0.7589 (m-80) cc_final: 0.6997 (m-80)
REVERT: C  561 ASN cc_start: 0.9165 (m-40) cc_final: 0.8776 (t0)
REVERT: C  574 MET cc_start: 0.8059 (mmm) cc_final: 0.7582 (mmm)
REVERT: C  589 LYS cc_start: 0.8609 (ttmt) cc_final: 0.8244 (mmtt)
REVERT: C  677 MET cc_start: 0.7522 (mtp) cc_final: 0.7295 (mtm)
REVERT: D  122 ARG cc_start: 0.8684 (ttm110) cc_final: 0.7753 (ttm110)
REVERT: D  159 MET cc_start: 0.7638 (mmm) cc_final: 0.7051 (mmp)
REVERT: D  173 MET cc_start: 0.8822 (mtt) cc_final: 0.8585 (mtt)
REVERT: D  255 GLN cc_start: 0.8391 (tm-30) cc_final: 0.7881 (tt0)
REVERT: D  308 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7116 (tm-30)
REVERT: D  495 MET cc_start: 0.7846 (mmt) cc_final: 0.7323 (tpp)
REVERT: D  501 GLU cc_start: 0.8633 (mm-30) cc_final: 0.7977 (mm-30)
REVERT: D  561 ASN cc_start: 0.9205 (m-40) cc_final: 0.8826 (t0)
REVERT: D  589 LYS cc_start: 0.8563 (ttmt) cc_final: 0.8184 (mmtt)
REVERT: D  635 LEU cc_start: 0.9364 (tp) cc_final: 0.9096 (tt)
REVERT: D  661 TYR cc_start: 0.9069 (t80) cc_final: 0.7922 (t80)
REVERT: D  677 MET cc_start: 0.7453 (mtp) cc_final: 0.7202 (mtm)
  outliers start: 1
  outliers final: 1
  residues processed: 349
  average time/residue: 0.1139
  time to fit residues: 63.9198
Evaluate side-chains
  240 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 239
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 240
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 148 optimal weight:    0.5980
   chunk 5 optimal weight:   10.0000
   chunk 135 optimal weight:    5.9990
   chunk 230 optimal weight:    0.7980
   chunk 175 optimal weight:    0.9990
   chunk 113 optimal weight:    0.9990
   chunk 70 optimal weight:    5.9990
   chunk 126 optimal weight:    0.9980
   chunk 168 optimal weight:    9.9990
   chunk 56 optimal weight:    0.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 523 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.116039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.091819 restraints weight = 40200.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.093672 restraints weight = 27802.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.094850 restraints weight = 21605.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.095863 restraints weight = 18303.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.096406 restraints weight = 16170.667|
|-----------------------------------------------------------------------------|
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.2456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  20060  Z= 0.098
  Angle     :  0.496   7.288  27120  Z= 0.256
  Chirality :  0.036   0.141   3100
  Planarity :  0.004   0.060   3360
  Dihedral  :  3.959  17.289   2620
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.44 (0.17), residues: 2376
  helix:  0.64 (0.13), residues: 1600
  sheet: -1.80 (0.68), residues: 68
  loop : -2.26 (0.22), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 226 
 TYR   0.013   0.001   TYR A 359 
 PHE   0.016   0.001   PHE B 193 
 TRP   0.012   0.001   TRP C 433 
 HIS   0.002   0.000   HIS C 430 

Details of bonding type rmsd
  covalent geometry    : bond        0.00211 (20060)
  covalent geometry    : angle       0.49582 (27120)
  hydrogen bonds       : bond        0.02852 ( 1084)
  hydrogen bonds       : angle       3.48869 ( 3192)

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

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

  4752 Ramachandran restraints generated.
    2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4752 Ramachandran restraints generated.
    2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  369 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 369
  time to evaluate  : 0.575 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 ARG cc_start: 0.8734 (ttm110) cc_final: 0.7808 (ttm110)
REVERT: A  173 MET cc_start: 0.8767 (mtt) cc_final: 0.8527 (mtt)
REVERT: A  255 GLN cc_start: 0.8327 (tm-30) cc_final: 0.7877 (tt0)
REVERT: A  306 VAL cc_start: 0.9156 (t) cc_final: 0.8874 (t)
REVERT: A  419 MET cc_start: 0.9022 (mtp) cc_final: 0.8747 (mtp)
REVERT: A  442 PHE cc_start: 0.8352 (t80) cc_final: 0.8135 (t80)
REVERT: A  495 MET cc_start: 0.8262 (mtt) cc_final: 0.7992 (mtp)
REVERT: A  501 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7830 (mm-30)
REVERT: A  561 ASN cc_start: 0.9133 (m-40) cc_final: 0.8805 (t0)
REVERT: A  572 MET cc_start: 0.8698 (mmm) cc_final: 0.8498 (mmm)
REVERT: A  589 LYS cc_start: 0.8596 (ttmt) cc_final: 0.8331 (mmtt)
REVERT: B  122 ARG cc_start: 0.8692 (ttm110) cc_final: 0.7881 (ttm110)
REVERT: B  255 GLN cc_start: 0.8344 (tm-30) cc_final: 0.7847 (tt0)
REVERT: B  562 MET cc_start: 0.8889 (mmm) cc_final: 0.8657 (tpp)
REVERT: B  592 PHE cc_start: 0.7933 (t80) cc_final: 0.7655 (t80)
REVERT: B  635 LEU cc_start: 0.9220 (tp) cc_final: 0.8906 (tt)
REVERT: B  661 TYR cc_start: 0.9089 (t80) cc_final: 0.8119 (t80)
REVERT: C  122 ARG cc_start: 0.8631 (ttm110) cc_final: 0.7735 (ttm110)
REVERT: C  255 GLN cc_start: 0.8327 (tm-30) cc_final: 0.7889 (tt0)
REVERT: C  306 VAL cc_start: 0.9197 (t) cc_final: 0.8854 (t)
REVERT: C  419 MET cc_start: 0.9010 (mtp) cc_final: 0.8758 (mtp)
REVERT: C  495 MET cc_start: 0.8227 (mtt) cc_final: 0.7966 (mtp)
REVERT: C  501 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7909 (mm-30)
REVERT: C  561 ASN cc_start: 0.9131 (m-40) cc_final: 0.8851 (t0)
REVERT: C  589 LYS cc_start: 0.8604 (ttmt) cc_final: 0.8219 (mmtt)
REVERT: C  592 PHE cc_start: 0.7788 (t80) cc_final: 0.7557 (t80)
REVERT: C  635 LEU cc_start: 0.9283 (tp) cc_final: 0.8985 (tt)
REVERT: D  122 ARG cc_start: 0.8646 (ttm110) cc_final: 0.7673 (ttm110)
REVERT: D  159 MET cc_start: 0.7594 (mmm) cc_final: 0.7022 (mmp)
REVERT: D  255 GLN cc_start: 0.8402 (tm-30) cc_final: 0.7831 (tt0)
REVERT: D  308 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7569 (tm-30)
REVERT: D  561 ASN cc_start: 0.9146 (m-40) cc_final: 0.8784 (t0)
REVERT: D  635 LEU cc_start: 0.9325 (tp) cc_final: 0.9106 (tt)
REVERT: D  645 GLN cc_start: 0.6620 (pm20) cc_final: 0.6412 (mm-40)
  outliers start: 0
  outliers final: 0
  residues processed: 369
  average time/residue: 0.1140
  time to fit residues: 67.4371
Evaluate side-chains
  251 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 251
  time to evaluate  : 0.855 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 240
   random chunks:
   chunk 5 optimal weight:    5.9990
   chunk 150 optimal weight:    0.9990
   chunk 75 optimal weight:    0.8980
   chunk 122 optimal weight:    8.9990
   chunk 16 optimal weight:    8.9990
   chunk 202 optimal weight:    3.9990
   chunk 101 optimal weight:    2.9990
   chunk 44 optimal weight:    5.9990
   chunk 71 optimal weight:    1.9990
   chunk 193 optimal weight:   10.0000
   chunk 229 optimal weight:    0.8980
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
A 143 GLN
** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 585 HIS
** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 523 HIS
D 585 HIS
D 646 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.114443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.090501 restraints weight = 40413.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.092051 restraints weight = 29675.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.093161 restraints weight = 24007.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.093695 restraints weight = 20734.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.094293 restraints weight = 18970.322|
|-----------------------------------------------------------------------------|
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.2637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  20060  Z= 0.125
  Angle     :  0.523   8.406  27120  Z= 0.270
  Chirality :  0.037   0.145   3100
  Planarity :  0.004   0.061   3360
  Dihedral  :  3.957  17.788   2620
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.24 (0.17), residues: 2376
  helix:  0.79 (0.13), residues: 1596
  sheet: -1.63 (0.71), residues: 68
  loop : -2.17 (0.22), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 716 
 TYR   0.012   0.001   TYR D 451 
 PHE   0.017   0.001   PHE C 193 
 TRP   0.013   0.001   TRP B 433 
 HIS   0.001   0.000   HIS A 523 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 (20060)
  covalent geometry    : angle       0.52341 (27120)
  hydrogen bonds       : bond        0.03118 ( 1084)
  hydrogen bonds       : angle       3.54089 ( 3192)

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

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

  4752 Ramachandran restraints generated.
    2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4752 Ramachandran restraints generated.
    2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  327 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 327
  time to evaluate  : 0.702 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 ARG cc_start: 0.8761 (ttm110) cc_final: 0.7759 (ttm110)
REVERT: A  173 MET cc_start: 0.8757 (mtt) cc_final: 0.8555 (mtt)
REVERT: A  255 GLN cc_start: 0.8346 (tm-30) cc_final: 0.7921 (tt0)
REVERT: A  495 MET cc_start: 0.8396 (mtt) cc_final: 0.8139 (mtp)
REVERT: A  501 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7878 (mm-30)
REVERT: A  561 ASN cc_start: 0.9221 (m-40) cc_final: 0.8911 (t0)
REVERT: A  562 MET cc_start: 0.9019 (mmm) cc_final: 0.8771 (tpp)
REVERT: A  574 MET cc_start: 0.7888 (mmm) cc_final: 0.7548 (mmm)
REVERT: A  589 LYS cc_start: 0.8570 (ttmt) cc_final: 0.8246 (mmtt)
REVERT: B  122 ARG cc_start: 0.8679 (ttm110) cc_final: 0.7931 (ttm110)
REVERT: B  255 GLN cc_start: 0.8375 (tm-30) cc_final: 0.7928 (tt0)
REVERT: C  122 ARG cc_start: 0.8626 (ttm110) cc_final: 0.7706 (ttm110)
REVERT: C  255 GLN cc_start: 0.8344 (tm-30) cc_final: 0.7963 (tt0)
REVERT: C  419 MET cc_start: 0.9078 (mtp) cc_final: 0.8849 (mtp)
REVERT: C  495 MET cc_start: 0.8337 (mtt) cc_final: 0.8090 (mtp)
REVERT: C  501 GLU cc_start: 0.8364 (mm-30) cc_final: 0.7905 (mm-30)
REVERT: C  561 ASN cc_start: 0.9250 (m-40) cc_final: 0.8924 (t0)
REVERT: C  589 LYS cc_start: 0.8645 (ttmt) cc_final: 0.8213 (mmtt)
REVERT: C  592 PHE cc_start: 0.7834 (t80) cc_final: 0.7601 (t80)
REVERT: D  122 ARG cc_start: 0.8661 (ttm110) cc_final: 0.7685 (ttm110)
REVERT: D  173 MET cc_start: 0.8759 (mtt) cc_final: 0.8530 (mtt)
REVERT: D  255 GLN cc_start: 0.8414 (tm-30) cc_final: 0.7890 (tt0)
REVERT: D  308 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7461 (tm-30)
REVERT: D  501 GLU cc_start: 0.8576 (mm-30) cc_final: 0.7892 (mm-30)
REVERT: D  561 ASN cc_start: 0.9238 (m-40) cc_final: 0.8825 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 327
  average time/residue: 0.1230
  time to fit residues: 63.4332
Evaluate side-chains
  227 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 227
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 240
   random chunks:
   chunk 193 optimal weight:    0.8980
   chunk 87 optimal weight:    4.9990
   chunk 17 optimal weight:    9.9990
   chunk 143 optimal weight:    2.9990
   chunk 48 optimal weight:    9.9990
   chunk 222 optimal weight:    0.9990
   chunk 113 optimal weight:    0.7980
   chunk 187 optimal weight:   10.0000
   chunk 91 optimal weight:    2.9990
   chunk 82 optimal weight:    3.9990
   chunk 215 optimal weight:    5.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
A 197 ASN
** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 216 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 = 0.3497 r_free = 0.3497 target = 0.114107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.090076 restraints weight = 40455.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.091631 restraints weight = 29867.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.092686 restraints weight = 24296.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.093171 restraints weight = 21054.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.093911 restraints weight = 19359.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.2781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  20060  Z= 0.133
  Angle     :  0.537   8.745  27120  Z= 0.276
  Chirality :  0.038   0.143   3100
  Planarity :  0.004   0.069   3360
  Dihedral  :  4.002  18.025   2620
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  1.60 %
    Favored  : 98.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.12 (0.18), residues: 2376
  helix:  0.85 (0.13), residues: 1600
  sheet: -1.67 (0.72), residues: 68
  loop : -2.03 (0.23), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG D 188 
 TYR   0.013   0.001   TYR B 594 
 PHE   0.019   0.001   PHE B 193 
 TRP   0.013   0.001   TRP C 433 
 HIS   0.002   0.001   HIS B 585 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (20060)
  covalent geometry    : angle       0.53696 (27120)
  hydrogen bonds       : bond        0.03174 ( 1084)
  hydrogen bonds       : angle       3.55561 ( 3192)

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

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

  4752 Ramachandran restraints generated.
    2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4752 Ramachandran restraints generated.
    2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  326 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 325
  time to evaluate  : 0.682 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 ARG cc_start: 0.8721 (ttm110) cc_final: 0.7736 (ttm110)
REVERT: A  173 MET cc_start: 0.8756 (mtt) cc_final: 0.8555 (mtt)
REVERT: A  255 GLN cc_start: 0.8329 (tm-30) cc_final: 0.7898 (tt0)
REVERT: A  501 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7775 (mm-30)
REVERT: A  561 ASN cc_start: 0.9191 (m-40) cc_final: 0.8921 (t0)
REVERT: A  562 MET cc_start: 0.9000 (mmm) cc_final: 0.8792 (tpp)
REVERT: A  574 MET cc_start: 0.7909 (mmm) cc_final: 0.7530 (mmm)
REVERT: A  589 LYS cc_start: 0.8599 (ttmt) cc_final: 0.8262 (mmtt)
REVERT: B  122 ARG cc_start: 0.8635 (ttm110) cc_final: 0.7901 (ttm110)
REVERT: B  255 GLN cc_start: 0.8424 (tm-30) cc_final: 0.7903 (tt0)
REVERT: B  562 MET cc_start: 0.8885 (mmm) cc_final: 0.8674 (tpp)
REVERT: C  122 ARG cc_start: 0.8591 (ttm110) cc_final: 0.7688 (ttm110)
REVERT: C  255 GLN cc_start: 0.8369 (tm-30) cc_final: 0.7979 (tt0)
REVERT: C  419 MET cc_start: 0.9056 (mtp) cc_final: 0.8800 (mtp)
REVERT: C  495 MET cc_start: 0.8185 (mtt) cc_final: 0.7972 (mtp)
REVERT: C  501 GLU cc_start: 0.8340 (mm-30) cc_final: 0.8022 (mm-30)
REVERT: C  561 ASN cc_start: 0.9260 (m-40) cc_final: 0.8999 (t0)
REVERT: C  562 MET cc_start: 0.8978 (mmm) cc_final: 0.8720 (tpp)
REVERT: D  122 ARG cc_start: 0.8636 (ttm110) cc_final: 0.7670 (ttm110)
REVERT: D  173 MET cc_start: 0.8712 (mtt) cc_final: 0.8481 (mtt)
REVERT: D  255 GLN cc_start: 0.8402 (tm-30) cc_final: 0.7893 (tt0)
REVERT: D  308 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7519 (tm-30)
REVERT: D  561 ASN cc_start: 0.9252 (m-40) cc_final: 0.8929 (t0)
REVERT: D  562 MET cc_start: 0.8955 (mmm) cc_final: 0.8712 (tpp)
REVERT: D  702 GLU cc_start: 0.7515 (tp30) cc_final: 0.7166 (tm-30)
REVERT: D  706 MET cc_start: 0.8456 (ttm) cc_final: 0.8253 (ttm)
  outliers start: 1
  outliers final: 0
  residues processed: 326
  average time/residue: 0.1138
  time to fit residues: 60.1396
Evaluate side-chains
  233 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 233
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 240
   random chunks:
   chunk 119 optimal weight:    1.9990
   chunk 233 optimal weight:    0.6980
   chunk 190 optimal weight:    0.6980
   chunk 145 optimal weight:    4.9990
   chunk 5 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   chunk 12 optimal weight:   20.0000
   chunk 234 optimal weight:    0.9990
   chunk 8 optimal weight:    9.9990
   chunk 123 optimal weight:   10.0000
   chunk 93 optimal weight:    5.9990
   overall best weight:    1.8786

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

Flipped N/Q/H residues before XYZ refinement:
A 197 ASN
** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 523 HIS
A 585 HIS
** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 585 HIS
D 197 ASN
** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 430 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.113942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.089845 restraints weight = 40522.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.091455 restraints weight = 29946.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.092537 restraints weight = 24074.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.093193 restraints weight = 20838.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.093610 restraints weight = 18949.451|
|-----------------------------------------------------------------------------|
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.2905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  20060  Z= 0.141
  Angle     :  0.553   8.196  27120  Z= 0.285
  Chirality :  0.038   0.146   3100
  Planarity :  0.004   0.059   3360
  Dihedral  :  4.059  17.381   2620
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.11 %
    Favored  : 92.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.01 (0.17), residues: 2376
  helix:  0.91 (0.13), residues: 1600
  sheet:  0.62 (0.86), residues: 48
  loop : -2.12 (0.22), residues: 728

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D 188 
 TYR   0.024   0.001   TYR D 564 
 PHE   0.021   0.001   PHE A 193 
 TRP   0.013   0.001   TRP B 433 
 HIS   0.002   0.001   HIS B 417 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (20060)
  covalent geometry    : angle       0.55260 (27120)
  hydrogen bonds       : bond        0.03302 ( 1084)
  hydrogen bonds       : angle       3.62055 ( 3192)

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

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

  4752 Ramachandran restraints generated.
    2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4752 Ramachandran restraints generated.
    2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  320 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 320
  time to evaluate  : 0.609 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 ARG cc_start: 0.8712 (ttm110) cc_final: 0.7728 (ttm110)
REVERT: A  255 GLN cc_start: 0.8372 (tm-30) cc_final: 0.7937 (tt0)
REVERT: A  306 VAL cc_start: 0.9144 (t) cc_final: 0.8875 (t)
REVERT: A  495 MET cc_start: 0.8351 (mtt) cc_final: 0.7978 (mtp)
REVERT: A  589 LYS cc_start: 0.8664 (ttmt) cc_final: 0.8230 (mmtt)
REVERT: B  122 ARG cc_start: 0.8593 (ttm110) cc_final: 0.7847 (ttm110)
REVERT: B  255 GLN cc_start: 0.8410 (tm-30) cc_final: 0.7908 (tt0)
REVERT: C  122 ARG cc_start: 0.8556 (ttm110) cc_final: 0.7675 (ttm110)
REVERT: C  255 GLN cc_start: 0.8373 (tm-30) cc_final: 0.7979 (tt0)
REVERT: C  419 MET cc_start: 0.9065 (mtp) cc_final: 0.8788 (mtp)
REVERT: C  495 MET cc_start: 0.8229 (mtt) cc_final: 0.8009 (mtp)
REVERT: C  501 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7858 (mm-30)
REVERT: C  589 LYS cc_start: 0.8566 (ttmt) cc_final: 0.8159 (mmtt)
REVERT: D  122 ARG cc_start: 0.8616 (ttm110) cc_final: 0.7667 (ttm110)
REVERT: D  173 MET cc_start: 0.8735 (mtt) cc_final: 0.8525 (mtt)
REVERT: D  255 GLN cc_start: 0.8405 (tm-30) cc_final: 0.7895 (tt0)
REVERT: D  308 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7522 (tm-30)
REVERT: D  635 LEU cc_start: 0.9400 (tp) cc_final: 0.9148 (tt)
REVERT: D  702 GLU cc_start: 0.7566 (tp30) cc_final: 0.7097 (tm-30)
REVERT: D  706 MET cc_start: 0.8457 (ttm) cc_final: 0.7998 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 320
  average time/residue: 0.1134
  time to fit residues: 58.6865
Evaluate side-chains
  228 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 228
  time to evaluate  : 0.539 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 240
   random chunks:
   chunk 9 optimal weight:    8.9990
   chunk 24 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   chunk 217 optimal weight:    7.9990
   chunk 84 optimal weight:    3.9990
   chunk 216 optimal weight:    8.9990
   chunk 180 optimal weight:   20.0000
   chunk 63 optimal weight:    2.9990
   chunk 13 optimal weight:   10.0000
   chunk 208 optimal weight:    0.0070
   chunk 151 optimal weight:    0.8980
   overall best weight:    1.7802

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

Flipped N/Q/H residues before XYZ refinement:
** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 561 ASN
** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 561 ASN
** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 523 HIS
** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 561 ASN
D 646 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.114310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.089344 restraints weight = 40588.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.091190 restraints weight = 28317.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.092462 restraints weight = 22133.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.093107 restraints weight = 18738.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.093809 restraints weight = 16929.769|
|-----------------------------------------------------------------------------|
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start:          0.3061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  20060  Z= 0.139
  Angle     :  0.558  10.006  27120  Z= 0.287
  Chirality :  0.038   0.143   3100
  Planarity :  0.004   0.056   3360
  Dihedral  :  4.048  17.009   2620
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.48 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.02 (0.17), residues: 2376
  helix:  0.92 (0.13), residues: 1600
  sheet:  0.63 (0.87), residues: 48
  loop : -2.09 (0.22), residues: 728

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D 188 
 TYR   0.011   0.001   TYR B 359 
 PHE   0.022   0.001   PHE D 193 
 TRP   0.011   0.001   TRP D 433 
 HIS   0.002   0.001   HIS C 585 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 (20060)
  covalent geometry    : angle       0.55816 (27120)
  hydrogen bonds       : bond        0.03287 ( 1084)
  hydrogen bonds       : angle       3.63195 ( 3192)

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

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

  4752 Ramachandran restraints generated.
    2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4752 Ramachandran restraints generated.
    2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  326 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 326
  time to evaluate  : 0.802 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 ARG cc_start: 0.8738 (ttm110) cc_final: 0.7749 (ttm110)
REVERT: A  255 GLN cc_start: 0.8384 (tm-30) cc_final: 0.7947 (tt0)
REVERT: A  495 MET cc_start: 0.8454 (mtt) cc_final: 0.8054 (mtp)
REVERT: A  574 MET cc_start: 0.8121 (mmt) cc_final: 0.7914 (mmm)
REVERT: A  589 LYS cc_start: 0.8661 (ttmt) cc_final: 0.8231 (mmtt)
REVERT: A  592 PHE cc_start: 0.8204 (t80) cc_final: 0.7879 (t80)
REVERT: B  122 ARG cc_start: 0.8613 (ttm110) cc_final: 0.7852 (ttm110)
REVERT: B  255 GLN cc_start: 0.8408 (tm-30) cc_final: 0.7907 (tt0)
REVERT: C  122 ARG cc_start: 0.8580 (ttm110) cc_final: 0.7674 (ttm110)
REVERT: C  255 GLN cc_start: 0.8373 (tm-30) cc_final: 0.7970 (tt0)
REVERT: C  306 VAL cc_start: 0.9116 (t) cc_final: 0.8832 (t)
REVERT: C  419 MET cc_start: 0.9098 (mtp) cc_final: 0.8846 (mtp)
REVERT: C  495 MET cc_start: 0.8316 (mtt) cc_final: 0.8079 (mtp)
REVERT: C  501 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7791 (mm-30)
REVERT: D  122 ARG cc_start: 0.8655 (ttm110) cc_final: 0.7680 (ttm110)
REVERT: D  255 GLN cc_start: 0.8411 (tm-30) cc_final: 0.7906 (tt0)
REVERT: D  308 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7498 (tm-30)
REVERT: D  592 PHE cc_start: 0.8131 (t80) cc_final: 0.7772 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 326
  average time/residue: 0.1143
  time to fit residues: 60.8950
Evaluate side-chains
  227 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 227
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 240
   random chunks:
   chunk 151 optimal weight:    2.9990
   chunk 147 optimal weight:    3.9990
   chunk 95 optimal weight:    3.9990
   chunk 41 optimal weight:    0.0170
   chunk 191 optimal weight:    3.9990
   chunk 167 optimal weight:    0.5980
   chunk 77 optimal weight:   10.0000
   chunk 179 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9980
   chunk 22 optimal weight:    0.5980
   chunk 60 optimal weight:   20.0000
   overall best weight:    1.0420

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

Flipped N/Q/H residues before XYZ refinement:
** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 561 ASN
D 216 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.115578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.091022 restraints weight = 39945.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.092930 restraints weight = 27466.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.094208 restraints weight = 21285.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.095126 restraints weight = 17890.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.095584 restraints weight = 15905.492|
|-----------------------------------------------------------------------------|
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.3197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  20060  Z= 0.107
  Angle     :  0.537   9.499  27120  Z= 0.275
  Chirality :  0.037   0.143   3100
  Planarity :  0.004   0.055   3360
  Dihedral  :  3.952  16.753   2620
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.13 (0.17), residues: 2376
  helix:  1.00 (0.13), residues: 1600
  sheet:  0.67 (0.86), residues: 48
  loop : -2.05 (0.22), residues: 728

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 188 
 TYR   0.017   0.001   TYR D 564 
 PHE   0.024   0.001   PHE A 193 
 TRP   0.010   0.001   TRP B 433 
 HIS   0.001   0.000   HIS B 417 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 (20060)
  covalent geometry    : angle       0.53654 (27120)
  hydrogen bonds       : bond        0.03010 ( 1084)
  hydrogen bonds       : angle       3.57947 ( 3192)

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

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

  4752 Ramachandran restraints generated.
    2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4752 Ramachandran restraints generated.
    2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  328 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 328
  time to evaluate  : 0.682 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 ARG cc_start: 0.8697 (ttm110) cc_final: 0.7750 (ttm110)
REVERT: A  159 MET cc_start: 0.8182 (mmp) cc_final: 0.7911 (mmm)
REVERT: A  255 GLN cc_start: 0.8379 (tm-30) cc_final: 0.7900 (tt0)
REVERT: A  306 VAL cc_start: 0.9143 (t) cc_final: 0.8904 (t)
REVERT: A  320 MET cc_start: 0.9167 (tpp) cc_final: 0.8928 (tpp)
REVERT: A  495 MET cc_start: 0.8344 (mtt) cc_final: 0.7975 (mtp)
REVERT: A  572 MET cc_start: 0.8724 (mmm) cc_final: 0.8142 (mmt)
REVERT: A  589 LYS cc_start: 0.8534 (ttmt) cc_final: 0.8172 (mmtt)
REVERT: A  592 PHE cc_start: 0.8086 (t80) cc_final: 0.7850 (t80)
REVERT: B  122 ARG cc_start: 0.8608 (ttm110) cc_final: 0.7801 (ttm110)
REVERT: B  255 GLN cc_start: 0.8403 (tm-30) cc_final: 0.7900 (tt0)
REVERT: B  306 VAL cc_start: 0.9243 (t) cc_final: 0.8516 (t)
REVERT: B  411 THR cc_start: 0.8459 (p) cc_final: 0.8078 (p)
REVERT: B  506 PHE cc_start: 0.7468 (m-80) cc_final: 0.7008 (m-80)
REVERT: C  122 ARG cc_start: 0.8551 (ttm110) cc_final: 0.7702 (ttm110)
REVERT: C  255 GLN cc_start: 0.8335 (tm-30) cc_final: 0.7911 (tt0)
REVERT: C  306 VAL cc_start: 0.9130 (t) cc_final: 0.8852 (t)
REVERT: C  419 MET cc_start: 0.9012 (mtp) cc_final: 0.8748 (mtp)
REVERT: C  589 LYS cc_start: 0.8564 (ttmt) cc_final: 0.8182 (mmtt)
REVERT: D  122 ARG cc_start: 0.8627 (ttm110) cc_final: 0.7681 (ttm110)
REVERT: D  255 GLN cc_start: 0.8294 (tm-30) cc_final: 0.7819 (tt0)
REVERT: D  635 LEU cc_start: 0.9352 (tp) cc_final: 0.9120 (tt)
REVERT: D  661 TYR cc_start: 0.9204 (t80) cc_final: 0.8995 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 328
  average time/residue: 0.1111
  time to fit residues: 58.7874
Evaluate side-chains
  239 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 239
  time to evaluate  : 0.732 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 240
   random chunks:
   chunk 137 optimal weight:   10.0000
   chunk 13 optimal weight:   10.0000
   chunk 77 optimal weight:    9.9990
   chunk 30 optimal weight:    2.9990
   chunk 161 optimal weight:    8.9990
   chunk 183 optimal weight:    0.4980
   chunk 118 optimal weight:    5.9990
   chunk 83 optimal weight:    6.9990
   chunk 220 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   chunk 43 optimal weight:    3.9990
   overall best weight:    2.2986

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

Flipped N/Q/H residues before XYZ refinement:
** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 452 ASN
** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 452 ASN
D 197 ASN
D 216 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.112946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.088026 restraints weight = 40669.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.089812 restraints weight = 28344.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.091034 restraints weight = 22202.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.091915 restraints weight = 18795.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.092342 restraints weight = 16730.893|
|-----------------------------------------------------------------------------|
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.3199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  20060  Z= 0.167
  Angle     :  0.607   9.842  27120  Z= 0.308
  Chirality :  0.039   0.144   3100
  Planarity :  0.004   0.092   3360
  Dihedral  :  4.103  16.584   2620
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.08 (0.17), residues: 2376
  helix:  0.97 (0.13), residues: 1600
  sheet:  0.65 (0.87), residues: 48
  loop : -2.06 (0.22), residues: 728

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 416 
 TYR   0.021   0.001   TYR D 564 
 PHE   0.015   0.001   PHE B 542 
 TRP   0.012   0.001   TRP B 433 
 HIS   0.003   0.001   HIS B 417 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 (20060)
  covalent geometry    : angle       0.60651 (27120)
  hydrogen bonds       : bond        0.03517 ( 1084)
  hydrogen bonds       : angle       3.73904 ( 3192)

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

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

  4752 Ramachandran restraints generated.
    2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4752 Ramachandran restraints generated.
    2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 298
  time to evaluate  : 0.715 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 ARG cc_start: 0.8727 (ttm110) cc_final: 0.7745 (ttm110)
REVERT: A  159 MET cc_start: 0.8141 (mmp) cc_final: 0.7855 (mmm)
REVERT: A  255 GLN cc_start: 0.8385 (tm-30) cc_final: 0.7947 (tt0)
REVERT: A  306 VAL cc_start: 0.9155 (t) cc_final: 0.8903 (t)
REVERT: A  495 MET cc_start: 0.8395 (mtt) cc_final: 0.8026 (mtp)
REVERT: A  572 MET cc_start: 0.8548 (mmm) cc_final: 0.8228 (mmt)
REVERT: A  589 LYS cc_start: 0.8562 (ttmt) cc_final: 0.8294 (mmtt)
REVERT: A  592 PHE cc_start: 0.8143 (t80) cc_final: 0.7724 (t80)
REVERT: B  122 ARG cc_start: 0.8596 (ttm110) cc_final: 0.7734 (ttm110)
REVERT: B  255 GLN cc_start: 0.8433 (tm-30) cc_final: 0.7901 (tt0)
REVERT: B  506 PHE cc_start: 0.7400 (m-80) cc_final: 0.6946 (m-80)
REVERT: B  592 PHE cc_start: 0.8213 (t80) cc_final: 0.7885 (t80)
REVERT: C  122 ARG cc_start: 0.8570 (ttm110) cc_final: 0.7693 (ttm110)
REVERT: C  255 GLN cc_start: 0.8350 (tm-30) cc_final: 0.7930 (tt0)
REVERT: C  419 MET cc_start: 0.9060 (mtp) cc_final: 0.8821 (mtp)
REVERT: C  495 MET cc_start: 0.8404 (mtt) cc_final: 0.7977 (mtp)
REVERT: D  122 ARG cc_start: 0.8663 (ttm110) cc_final: 0.7692 (ttm110)
REVERT: D  255 GLN cc_start: 0.8389 (tm-30) cc_final: 0.7874 (tt0)
REVERT: D  495 MET cc_start: 0.8398 (mtt) cc_final: 0.7962 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 298
  average time/residue: 0.1088
  time to fit residues: 53.3102
Evaluate side-chains
  220 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 220
  time to evaluate  : 0.681 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 240
   random chunks:
   chunk 13 optimal weight:    9.9990
   chunk 42 optimal weight:    0.9980
   chunk 220 optimal weight:    0.7980
   chunk 87 optimal weight:    4.9990
   chunk 179 optimal weight:    7.9990
   chunk 158 optimal weight:   10.0000
   chunk 228 optimal weight:    6.9990
   chunk 147 optimal weight:    1.9990
   chunk 226 optimal weight:    0.8980
   chunk 8 optimal weight:    5.9990
   chunk 118 optimal weight:    5.9990
   overall best weight:    1.9384

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

Flipped N/Q/H residues before XYZ refinement:
** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 452 ASN
** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 452 ASN
** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.113434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.088754 restraints weight = 40583.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.090507 restraints weight = 28472.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.091719 restraints weight = 22366.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.092411 restraints weight = 19007.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.093009 restraints weight = 17104.683|
|-----------------------------------------------------------------------------|
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.3256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  20060  Z= 0.147
  Angle     :  0.589   9.666  27120  Z= 0.299
  Chirality :  0.038   0.143   3100
  Planarity :  0.004   0.091   3360
  Dihedral  :  4.109  18.511   2620
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.08 (0.17), residues: 2376
  helix:  0.96 (0.13), residues: 1600
  sheet:  0.74 (0.89), residues: 48
  loop : -2.05 (0.22), residues: 728

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 416 
 TYR   0.012   0.001   TYR D 451 
 PHE   0.031   0.001   PHE C 193 
 TRP   0.012   0.001   TRP B 692 
 HIS   0.002   0.001   HIS D 430 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (20060)
  covalent geometry    : angle       0.58883 (27120)
  hydrogen bonds       : bond        0.03386 ( 1084)
  hydrogen bonds       : angle       3.73768 ( 3192)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2596.32 seconds
wall clock time: 46 minutes 52.08 seconds (2812.08 seconds total)