Starting phenix.real_space_refine
on Fri Jun 13 20:52:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7nmn_12466/06_2025/7nmn_12466.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7nmn_12466/06_2025/7nmn_12466.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7nmn_12466/06_2025/7nmn_12466.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7nmn_12466/06_2025/7nmn_12466.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7nmn_12466/06_2025/7nmn_12466.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7nmn_12466/06_2025/7nmn_12466.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.007
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     128      5.16       5
     C   10000      2.51       5
     N    2608      2.21       5
     O    2700      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 48 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 15436
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3859
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 469, 3859
          Classifications: {'peptide': 469}
          Link IDs: {'PTRANS': 16, 'TRANS': 452}
          Chain breaks: 1
  Restraints were copied for chains:
    C, B, D
  Time building chain proxies: 7.94, per 1000 atoms: 0.51
  Number of scatterers: 15436
  At special positions: 0
  Unit cell: (128.905, 128.905, 120.015, 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     128     16.00
     O    2700      8.00
     N    2608      7.00
     C   10000      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: 3.35
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  3720 Ramachandran restraints generated.
    1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3552

  Finding SS restraints...
    Secondary structure from input PDB file:
      84 helices and 8 sheets defined
      69.1% alpha, 5.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 219 through 223
    Processing helix  chain 'A' and resid 229 through 236
    Processing helix  chain 'A' and resid 237 through 252
      removed outlier: 4.069A  pdb=" N   GLY A 252 " --> pdb=" O   VAL A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 287
      removed outlier: 3.575A  pdb=" N   PHE A 264 " --> pdb=" O   SER A 260 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   GLY A 276 " --> pdb=" O   LEU A 272 " (cutoff:3.500A)
      Proline residue:  A 282  - end of helix
      removed outlier: 4.066A  pdb=" N   THR A 286 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 314
      removed outlier: 4.327A  pdb=" N   TRP A 296 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   VAL A 312 " --> pdb=" O   LEU A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 351
      removed outlier: 3.656A  pdb=" N   ILE A 334 " --> pdb=" O   ASP A 330 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   LYS A 340 " --> pdb=" O   MET A 336 " (cutoff:3.500A)
      removed outlier: 7.482A  pdb=" N   VAL A 344 " --> pdb=" O   LYS A 340 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   VAL A 345 " --> pdb=" O   SER A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 388
    Processing helix  chain 'A' and resid 391 through 407
      removed outlier: 3.696A  pdb=" N   LEU A 395 " --> pdb=" O   ARG A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 444
      Proline residue:  A 441  - end of helix
      removed outlier: 3.658A  pdb=" N   GLN A 444 " --> pdb=" O   VAL A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 455
    Processing helix  chain 'A' and resid 461 through 478
      removed outlier: 3.571A  pdb=" N   TYR A 466 " --> pdb=" O   TRP A 462 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 489 through 520
      removed outlier: 4.033A  pdb=" N   GLY A 512 " --> pdb=" O   ALA A 508 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   HIS A 513 " --> pdb=" O   MET A 509 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 543
      removed outlier: 3.738A  pdb=" N   ARG A 526 " --> pdb=" O   ASP A 522 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   HIS A 542 " --> pdb=" O   TYR A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 545 through 558
    Processing helix  chain 'A' and resid 566 through 574
      removed outlier: 3.627A  pdb=" N   ILE A 570 " --> pdb=" O   ASP A 566 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   LEU A 574 " --> pdb=" O   ILE A 570 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 575 through 592
      removed outlier: 3.581A  pdb=" N   ILE A 583 " --> pdb=" O   ARG A 579 " (cutoff:3.500A)
      removed outlier: 5.534A  pdb=" N   LYS A 589 " --> pdb=" O   PHE A 585 " (cutoff:3.500A)
      removed outlier: 5.624A  pdb=" N   LEU A 590 " --> pdb=" O   ASN A 586 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 601 through 609
    Processing helix  chain 'A' and resid 610 through 612
      No H-bonds generated for 'chain 'A' and resid 610 through 612'
    Processing helix  chain 'A' and resid 660 through 665
      removed outlier: 3.523A  pdb=" N   CYS A 663 " --> pdb=" O   GLY A 660 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 687 through 697
    Processing helix  chain 'A' and resid 697 through 706
    Processing helix  chain 'B' and resid 219 through 223
    Processing helix  chain 'B' and resid 229 through 236
    Processing helix  chain 'B' and resid 237 through 252
      removed outlier: 4.068A  pdb=" N   GLY B 252 " --> pdb=" O   VAL B 248 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 287
      removed outlier: 3.574A  pdb=" N   PHE B 264 " --> pdb=" O   SER B 260 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   GLY B 276 " --> pdb=" O   LEU B 272 " (cutoff:3.500A)
      Proline residue:  B 282  - end of helix
      removed outlier: 4.066A  pdb=" N   THR B 286 " --> pdb=" O   PRO B 282 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 292 through 314
      removed outlier: 4.327A  pdb=" N   TRP B 296 " --> pdb=" O   ASN B 292 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   VAL B 312 " --> pdb=" O   LEU B 308 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 330 through 351
      removed outlier: 3.655A  pdb=" N   ILE B 334 " --> pdb=" O   ASP B 330 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   LYS B 340 " --> pdb=" O   MET B 336 " (cutoff:3.500A)
      removed outlier: 7.482A  pdb=" N   VAL B 344 " --> pdb=" O   LYS B 340 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   VAL B 345 " --> pdb=" O   SER B 341 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 376 through 388
    Processing helix  chain 'B' and resid 391 through 407
      removed outlier: 3.695A  pdb=" N   LEU B 395 " --> pdb=" O   ARG B 391 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 444
      Proline residue:  B 441  - end of helix
      removed outlier: 3.657A  pdb=" N   GLN B 444 " --> pdb=" O   VAL B 440 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 450 through 455
    Processing helix  chain 'B' and resid 461 through 478
      removed outlier: 3.571A  pdb=" N   TYR B 466 " --> pdb=" O   TRP B 462 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 489 through 520
      removed outlier: 4.033A  pdb=" N   GLY B 512 " --> pdb=" O   ALA B 508 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   HIS B 513 " --> pdb=" O   MET B 509 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 522 through 543
      removed outlier: 3.738A  pdb=" N   ARG B 526 " --> pdb=" O   ASP B 522 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   HIS B 542 " --> pdb=" O   TYR B 538 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 545 through 558
    Processing helix  chain 'B' and resid 566 through 574
      removed outlier: 3.627A  pdb=" N   ILE B 570 " --> pdb=" O   ASP B 566 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   LEU B 574 " --> pdb=" O   ILE B 570 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 575 through 592
      removed outlier: 3.580A  pdb=" N   ILE B 583 " --> pdb=" O   ARG B 579 " (cutoff:3.500A)
      removed outlier: 5.534A  pdb=" N   LYS B 589 " --> pdb=" O   PHE B 585 " (cutoff:3.500A)
      removed outlier: 5.624A  pdb=" N   LEU B 590 " --> pdb=" O   ASN B 586 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 601 through 609
    Processing helix  chain 'B' and resid 610 through 612
      No H-bonds generated for 'chain 'B' and resid 610 through 612'
    Processing helix  chain 'B' and resid 660 through 665
      removed outlier: 3.523A  pdb=" N   CYS B 663 " --> pdb=" O   GLY B 660 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 687 through 697
    Processing helix  chain 'B' and resid 697 through 706
    Processing helix  chain 'C' and resid 219 through 223
    Processing helix  chain 'C' and resid 229 through 236
    Processing helix  chain 'C' and resid 237 through 252
      removed outlier: 4.070A  pdb=" N   GLY C 252 " --> pdb=" O   VAL C 248 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 260 through 287
      removed outlier: 3.574A  pdb=" N   PHE C 264 " --> pdb=" O   SER C 260 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   GLY C 276 " --> pdb=" O   LEU C 272 " (cutoff:3.500A)
      Proline residue:  C 282  - end of helix
      removed outlier: 4.066A  pdb=" N   THR C 286 " --> pdb=" O   PRO C 282 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 292 through 314
      removed outlier: 4.327A  pdb=" N   TRP C 296 " --> pdb=" O   ASN C 292 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   VAL C 312 " --> pdb=" O   LEU C 308 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 330 through 351
      removed outlier: 3.656A  pdb=" N   ILE C 334 " --> pdb=" O   ASP C 330 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   LYS C 340 " --> pdb=" O   MET C 336 " (cutoff:3.500A)
      removed outlier: 7.481A  pdb=" N   VAL C 344 " --> pdb=" O   LYS C 340 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   VAL C 345 " --> pdb=" O   SER C 341 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 376 through 388
    Processing helix  chain 'C' and resid 391 through 407
      removed outlier: 3.695A  pdb=" N   LEU C 395 " --> pdb=" O   ARG C 391 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 411 through 444
      Proline residue:  C 441  - end of helix
      removed outlier: 3.658A  pdb=" N   GLN C 444 " --> pdb=" O   VAL C 440 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 450 through 455
    Processing helix  chain 'C' and resid 461 through 478
      removed outlier: 3.572A  pdb=" N   TYR C 466 " --> pdb=" O   TRP C 462 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 489 through 520
      removed outlier: 4.033A  pdb=" N   GLY C 512 " --> pdb=" O   ALA C 508 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   HIS C 513 " --> pdb=" O   MET C 509 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 522 through 543
      removed outlier: 3.738A  pdb=" N   ARG C 526 " --> pdb=" O   ASP C 522 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   HIS C 542 " --> pdb=" O   TYR C 538 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 545 through 558
    Processing helix  chain 'C' and resid 566 through 574
      removed outlier: 3.627A  pdb=" N   ILE C 570 " --> pdb=" O   ASP C 566 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   LEU C 574 " --> pdb=" O   ILE C 570 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 575 through 592
      removed outlier: 3.581A  pdb=" N   ILE C 583 " --> pdb=" O   ARG C 579 " (cutoff:3.500A)
      removed outlier: 5.533A  pdb=" N   LYS C 589 " --> pdb=" O   PHE C 585 " (cutoff:3.500A)
      removed outlier: 5.623A  pdb=" N   LEU C 590 " --> pdb=" O   ASN C 586 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 601 through 609
    Processing helix  chain 'C' and resid 610 through 612
      No H-bonds generated for 'chain 'C' and resid 610 through 612'
    Processing helix  chain 'C' and resid 660 through 665
      removed outlier: 3.522A  pdb=" N   CYS C 663 " --> pdb=" O   GLY C 660 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 687 through 697
    Processing helix  chain 'C' and resid 697 through 706
    Processing helix  chain 'D' and resid 219 through 223
    Processing helix  chain 'D' and resid 229 through 236
    Processing helix  chain 'D' and resid 237 through 252
      removed outlier: 4.069A  pdb=" N   GLY D 252 " --> pdb=" O   VAL D 248 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 260 through 287
      removed outlier: 3.575A  pdb=" N   PHE D 264 " --> pdb=" O   SER D 260 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   GLY D 276 " --> pdb=" O   LEU D 272 " (cutoff:3.500A)
      Proline residue:  D 282  - end of helix
      removed outlier: 4.066A  pdb=" N   THR D 286 " --> pdb=" O   PRO D 282 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 292 through 314
      removed outlier: 4.327A  pdb=" N   TRP D 296 " --> pdb=" O   ASN D 292 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   VAL D 312 " --> pdb=" O   LEU D 308 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 330 through 351
      removed outlier: 3.655A  pdb=" N   ILE D 334 " --> pdb=" O   ASP D 330 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   LYS D 340 " --> pdb=" O   MET D 336 " (cutoff:3.500A)
      removed outlier: 7.481A  pdb=" N   VAL D 344 " --> pdb=" O   LYS D 340 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   VAL D 345 " --> pdb=" O   SER D 341 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 376 through 388
    Processing helix  chain 'D' and resid 391 through 407
      removed outlier: 3.696A  pdb=" N   LEU D 395 " --> pdb=" O   ARG D 391 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 411 through 444
      Proline residue:  D 441  - end of helix
      removed outlier: 3.658A  pdb=" N   GLN D 444 " --> pdb=" O   VAL D 440 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 450 through 455
    Processing helix  chain 'D' and resid 461 through 478
      removed outlier: 3.572A  pdb=" N   TYR D 466 " --> pdb=" O   TRP D 462 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 489 through 520
      removed outlier: 4.033A  pdb=" N   GLY D 512 " --> pdb=" O   ALA D 508 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   HIS D 513 " --> pdb=" O   MET D 509 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 522 through 543
      removed outlier: 3.738A  pdb=" N   ARG D 526 " --> pdb=" O   ASP D 522 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   HIS D 542 " --> pdb=" O   TYR D 538 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 545 through 558
    Processing helix  chain 'D' and resid 566 through 574
      removed outlier: 3.627A  pdb=" N   ILE D 570 " --> pdb=" O   ASP D 566 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   LEU D 574 " --> pdb=" O   ILE D 570 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 575 through 592
      removed outlier: 3.581A  pdb=" N   ILE D 583 " --> pdb=" O   ARG D 579 " (cutoff:3.500A)
      removed outlier: 5.533A  pdb=" N   LYS D 589 " --> pdb=" O   PHE D 585 " (cutoff:3.500A)
      removed outlier: 5.624A  pdb=" N   LEU D 590 " --> pdb=" O   ASN D 586 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 601 through 609
    Processing helix  chain 'D' and resid 610 through 612
      No H-bonds generated for 'chain 'D' and resid 610 through 612'
    Processing helix  chain 'D' and resid 660 through 665
      removed outlier: 3.523A  pdb=" N   CYS D 663 " --> pdb=" O   GLY D 660 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 687 through 697
    Processing helix  chain 'D' and resid 697 through 706
    Processing sheet with id=AA1, first strand: chain 'A' and resid 613 through 617
    Processing sheet with id=AA2, first strand: chain 'A' and resid 651 through 654
      removed outlier: 3.609A  pdb=" N   SER A 673 " --> pdb=" O   LEU A 644 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 613 through 617
    Processing sheet with id=AA4, first strand: chain 'B' and resid 651 through 654
      removed outlier: 3.610A  pdb=" N   SER B 673 " --> pdb=" O   LEU B 644 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 613 through 617
    Processing sheet with id=AA6, first strand: chain 'C' and resid 651 through 654
      removed outlier: 3.610A  pdb=" N   SER C 673 " --> pdb=" O   LEU C 644 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 613 through 617
    Processing sheet with id=AA8, first strand: chain 'D' and resid 651 through 654
      removed outlier: 3.609A  pdb=" N   SER D 673 " --> pdb=" O   LEU D 644 " (cutoff:3.500A)

    932 hydrogen bonds defined for protein.
    2712 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: 4.52

  Time building geometry restraints manager: 4.01 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3081
        1.33 -     1.45: 3873
        1.45 -     1.57: 8634
        1.57 -     1.69: 0
        1.69 -     1.81: 224
  Bond restraints: 15812
  Sorted by residual:
  bond pdb=" N   LEU B 665 "
       pdb=" CA  LEU B 665 "
    ideal  model  delta    sigma   weight residual
    1.456  1.503 -0.047 1.35e-02 5.49e+03 1.21e+01
  bond pdb=" N   LEU D 665 "
       pdb=" CA  LEU D 665 "
    ideal  model  delta    sigma   weight residual
    1.456  1.502 -0.047 1.35e-02 5.49e+03 1.20e+01
  bond pdb=" N   LEU A 665 "
       pdb=" CA  LEU A 665 "
    ideal  model  delta    sigma   weight residual
    1.456  1.502 -0.046 1.35e-02 5.49e+03 1.19e+01
  bond pdb=" N   LEU C 665 "
       pdb=" CA  LEU C 665 "
    ideal  model  delta    sigma   weight residual
    1.456  1.502 -0.046 1.35e-02 5.49e+03 1.16e+01
  bond pdb=" N   ILE B 399 "
       pdb=" CA  ILE B 399 "
    ideal  model  delta    sigma   weight residual
    1.461  1.498 -0.037 1.17e-02 7.31e+03 9.84e+00
  ... (remaining 15807 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.97: 19154
        1.97 -     3.95: 2036
        3.95 -     5.92: 138
        5.92 -     7.89: 15
        7.89 -     9.87: 13
  Bond angle restraints: 21356
  Sorted by residual:
  angle pdb=" C   ASN D 459 "
        pdb=" CA  ASN D 459 "
        pdb=" CB  ASN D 459 "
      ideal   model   delta    sigma   weight residual
     110.19  120.06   -9.87 1.62e+00 3.81e-01 3.71e+01
  angle pdb=" C   ASN A 459 "
        pdb=" CA  ASN A 459 "
        pdb=" CB  ASN A 459 "
      ideal   model   delta    sigma   weight residual
     110.19  120.04   -9.85 1.62e+00 3.81e-01 3.70e+01
  angle pdb=" C   ASN C 459 "
        pdb=" CA  ASN C 459 "
        pdb=" CB  ASN C 459 "
      ideal   model   delta    sigma   weight residual
     110.19  120.03   -9.84 1.62e+00 3.81e-01 3.69e+01
  angle pdb=" C   ASN B 459 "
        pdb=" CA  ASN B 459 "
        pdb=" CB  ASN B 459 "
      ideal   model   delta    sigma   weight residual
     110.19  120.01   -9.82 1.62e+00 3.81e-01 3.67e+01
  angle pdb=" CA  HIS D 400 "
        pdb=" C   HIS D 400 "
        pdb=" O   HIS D 400 "
      ideal   model   delta    sigma   weight residual
     120.82  115.77    5.05 1.05e+00 9.07e-01 2.31e+01
  ... (remaining 21351 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.99: 8372
       16.99 -    33.98: 836
       33.98 -    50.97: 156
       50.97 -    67.96: 44
       67.96 -    84.95: 8
  Dihedral angle restraints: 9416
    sinusoidal: 3912
      harmonic: 5504
  Sorted by residual:
  dihedral pdb=" C   ASN D 459 "
           pdb=" N   ASN D 459 "
           pdb=" CA  ASN D 459 "
           pdb=" CB  ASN D 459 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -136.06   13.46     0      2.50e+00 1.60e-01 2.90e+01
  dihedral pdb=" C   ASN A 459 "
           pdb=" N   ASN A 459 "
           pdb=" CA  ASN A 459 "
           pdb=" CB  ASN A 459 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -136.02   13.42     0      2.50e+00 1.60e-01 2.88e+01
  dihedral pdb=" C   ASN B 459 "
           pdb=" N   ASN B 459 "
           pdb=" CA  ASN B 459 "
           pdb=" CB  ASN B 459 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -135.99   13.39     0      2.50e+00 1.60e-01 2.87e+01
  ... (remaining 9413 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.077: 1591
       0.077 -    0.153: 605
       0.153 -    0.230: 120
       0.230 -    0.307: 8
       0.307 -    0.384: 4
  Chirality restraints: 2328
  Sorted by residual:
  chirality pdb=" CA  ASN D 459 "
            pdb=" N   ASN D 459 "
            pdb=" C   ASN D 459 "
            pdb=" CB  ASN D 459 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.68e+00
  chirality pdb=" CA  ASN A 459 "
            pdb=" N   ASN A 459 "
            pdb=" C   ASN A 459 "
            pdb=" CB  ASN A 459 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.65e+00
  chirality pdb=" CA  ASN B 459 "
            pdb=" N   ASN B 459 "
            pdb=" C   ASN B 459 "
            pdb=" CB  ASN B 459 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.62e+00
  ... (remaining 2325 not shown)

  Planarity restraints: 2684
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG D 397 "    0.015 2.00e-02 2.50e+03   3.06e-02 9.39e+00
        pdb=" C   ARG D 397 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   ARG D 397 "    0.020 2.00e-02 2.50e+03
        pdb=" N   TYR D 398 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 397 "   -0.015 2.00e-02 2.50e+03   3.05e-02 9.31e+00
        pdb=" C   ARG A 397 "    0.053 2.00e-02 2.50e+03
        pdb=" O   ARG A 397 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   TYR A 398 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 397 "   -0.015 2.00e-02 2.50e+03   3.05e-02 9.29e+00
        pdb=" C   ARG B 397 "    0.053 2.00e-02 2.50e+03
        pdb=" O   ARG B 397 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   TYR B 398 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 2681 not shown)

  Histogram of nonbonded interaction distances:
        2.36 -     2.87: 5560
        2.87 -     3.38: 14687
        3.38 -     3.88: 24227
        3.88 -     4.39: 26319
        4.39 -     4.90: 46009
  Nonbonded interactions: 116802
  Sorted by model distance:
  nonbonded pdb=" N   ASP A 326 "
            pdb=" OD1 ASP A 326 "
     model   vdw
     2.361 3.120
  nonbonded pdb=" N   ASP C 326 "
            pdb=" OD1 ASP C 326 "
     model   vdw
     2.361 3.120
  nonbonded pdb=" N   ASP B 326 "
            pdb=" OD1 ASP B 326 "
     model   vdw
     2.362 3.120
  nonbonded pdb=" N   ASP D 326 "
            pdb=" OD1 ASP D 326 "
     model   vdw
     2.362 3.120
  nonbonded pdb=" O   ASN A 459 "
            pdb=" OD1 ASN A 459 "
     model   vdw
     2.367 3.040
  ... (remaining 116797 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: 0.12
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  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:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.600
  Check model and map are aligned:         0.110
  Set scattering table:                    0.160
  Process input model:                     32.170
  Find NCS groups from input model:        0.290
  Set up NCS constraints:                  0.050
  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:2.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
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      :  0.010   0.070  15812  Z= 0.622
  Angle     :  1.163   9.867  21356  Z= 0.816
  Chirality :  0.079   0.384   2328
  Planarity :  0.008   0.075   2684
  Dihedral  : 14.026  84.953   5864
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 15.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 12.53 %
    Favored  : 86.59 %
  Cbeta Deviations :  0.23 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.43 (0.18), residues: 1860
  helix: -0.35 (0.14), residues: 1176
  sheet: -1.13 (0.35), residues: 132
  loop : -1.97 (0.23), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 451 
 HIS   0.006   0.002   HIS B 407 
 PHE   0.020   0.002   PHE C 253 
 TYR   0.016   0.002   TYR D 556 
 ARG   0.012   0.001   ARG B 217 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16158 (  932)
  hydrogen bonds       : angle       6.22300 ( 2712)
  covalent geometry    : bond        0.00984 (15812)
  covalent geometry    : angle       1.16299 (21356)

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

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

  3720 Ramachandran restraints generated.
    1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3720 Ramachandran restraints generated.
    1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  306 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 291
  time to evaluate  : 1.618 
Fit side-chains
REVERT: A  433 ASP cc_start: 0.7950 (t0) cc_final: 0.7725 (t0)
REVERT: A  679 TYR cc_start: 0.8133 (m-80) cc_final: 0.7878 (m-80)
REVERT: A  696 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7735 (mm-30)
REVERT: B  433 ASP cc_start: 0.7980 (t0) cc_final: 0.7750 (t0)
REVERT: B  460 ASN cc_start: 0.8513 (OUTLIER) cc_final: 0.8305 (m-40)
REVERT: B  696 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7731 (mm-30)
REVERT: C  433 ASP cc_start: 0.8020 (t0) cc_final: 0.7787 (t0)
REVERT: C  460 ASN cc_start: 0.8508 (OUTLIER) cc_final: 0.8277 (m-40)
REVERT: C  696 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7684 (mm-30)
REVERT: D  433 ASP cc_start: 0.8007 (t0) cc_final: 0.7769 (t0)
REVERT: D  460 ASN cc_start: 0.8515 (OUTLIER) cc_final: 0.8260 (m-40)
  outliers start: 15
  outliers final: 8
  residues processed: 306
  average time/residue: 0.2743
  time to fit residues: 122.4591
Evaluate side-chains
  222 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 208
  time to evaluate  : 1.659 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  400 HIS
Chi-restraints excluded: chain A residue  480 ILE
Chi-restraints excluded: chain A residue  696 GLU
Chi-restraints excluded: chain B residue  400 HIS
Chi-restraints excluded: chain B residue  460 ASN
Chi-restraints excluded: chain B residue  480 ILE
Chi-restraints excluded: chain B residue  696 GLU
Chi-restraints excluded: chain C residue  400 HIS
Chi-restraints excluded: chain C residue  460 ASN
Chi-restraints excluded: chain C residue  480 ILE
Chi-restraints excluded: chain C residue  696 GLU
Chi-restraints excluded: chain D residue  400 HIS
Chi-restraints excluded: chain D residue  460 ASN
Chi-restraints excluded: chain D residue  480 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 155 optimal weight:    1.9990
   chunk 139 optimal weight:    5.9990
   chunk 77 optimal weight:    0.8980
   chunk 47 optimal weight:    7.9990
   chunk 94 optimal weight:    6.9990
   chunk 74 optimal weight:    0.8980
   chunk 144 optimal weight:    3.9990
   chunk 55 optimal weight:    3.9990
   chunk 87 optimal weight:    4.9990
   chunk 107 optimal weight:    9.9990
   chunk 167 optimal weight:    0.8980
   overall best weight:    1.7384

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

Flipped N/Q/H residues before XYZ refinement:
A 245 GLN
A 444 GLN
A 455 ASN
A 459 ASN
A 460 ASN
A 519 GLN
A 537 GLN
A 542 HIS
A 586 ASN
B 245 GLN
B 444 GLN
B 455 ASN
B 459 ASN
B 519 GLN
B 542 HIS
B 586 ASN
B 603 ASN
C 245 GLN
C 444 GLN
C 455 ASN
C 459 ASN
C 519 GLN
C 537 GLN
C 542 HIS
C 586 ASN
C 603 ASN
C 691 ASN
D 245 GLN
D 444 GLN
D 455 ASN
D 459 ASN
D 519 GLN
D 542 HIS
D 586 ASN
D 603 ASN

Total number of N/Q/H flips: 35

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.164557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.127740 restraints weight = 21305.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.128560 restraints weight = 15435.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.129686 restraints weight = 11988.128|
|-----------------------------------------------------------------------------|
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.2064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  15812  Z= 0.150
  Angle     :  0.576   6.301  21356  Z= 0.302
  Chirality :  0.039   0.123   2328
  Planarity :  0.005   0.049   2684
  Dihedral  :  6.287  77.936   2111
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 14.24 %
    Favored  : 83.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.19), residues: 1860
  helix:  1.31 (0.15), residues: 1156
  sheet: -0.76 (0.38), residues: 132
  loop : -1.45 (0.25), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 462 
 HIS   0.003   0.001   HIS A 513 
 PHE   0.011   0.001   PHE D 659 
 TYR   0.009   0.001   TYR D 532 
 ARG   0.003   0.000   ARG D 588 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05069 (  932)
  hydrogen bonds       : angle       4.14236 ( 2712)
  covalent geometry    : bond        0.00335 (15812)
  covalent geometry    : angle       0.57583 (21356)

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

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

  3720 Ramachandran restraints generated.
    1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3720 Ramachandran restraints generated.
    1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 245
  time to evaluate  : 1.689 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 ASP cc_start: 0.8444 (m-30) cc_final: 0.8191 (m-30)
REVERT: A  270 MET cc_start: 0.8251 (mmm) cc_final: 0.8006 (mmm)
REVERT: A  433 ASP cc_start: 0.8248 (t0) cc_final: 0.7976 (t0)
REVERT: B  233 ARG cc_start: 0.8028 (tmm-80) cc_final: 0.7755 (ttt180)
REVERT: B  267 ASP cc_start: 0.8497 (m-30) cc_final: 0.8288 (m-30)
REVERT: B  433 ASP cc_start: 0.8239 (t0) cc_final: 0.7975 (t0)
REVERT: C  233 ARG cc_start: 0.7983 (tmm-80) cc_final: 0.7760 (ttt180)
REVERT: C  433 ASP cc_start: 0.8217 (t0) cc_final: 0.7969 (t0)
REVERT: D  222 MET cc_start: 0.6776 (mtt) cc_final: 0.6304 (mtm)
REVERT: D  233 ARG cc_start: 0.8044 (tmm-80) cc_final: 0.7745 (ttt180)
REVERT: D  267 ASP cc_start: 0.8485 (m-30) cc_final: 0.8273 (m-30)
REVERT: D  270 MET cc_start: 0.8314 (mmm) cc_final: 0.8050 (mmm)
REVERT: D  402 TRP cc_start: 0.7613 (m100) cc_final: 0.7407 (m100)
REVERT: D  433 ASP cc_start: 0.8247 (t0) cc_final: 0.7970 (t0)
  outliers start: 47
  outliers final: 22
  residues processed: 284
  average time/residue: 0.2983
  time to fit residues: 120.6051
Evaluate side-chains
  238 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 216
  time to evaluate  : 1.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  400 HIS
Chi-restraints excluded: chain A residue  610 THR
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  678 THR
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain B residue  400 HIS
Chi-restraints excluded: chain B residue  610 THR
Chi-restraints excluded: chain B residue  674 VAL
Chi-restraints excluded: chain C residue  272 LEU
Chi-restraints excluded: chain C residue  328 ILE
Chi-restraints excluded: chain C residue  400 HIS
Chi-restraints excluded: chain C residue  610 THR
Chi-restraints excluded: chain C residue  674 VAL
Chi-restraints excluded: chain C residue  678 THR
Chi-restraints excluded: chain D residue  272 LEU
Chi-restraints excluded: chain D residue  328 ILE
Chi-restraints excluded: chain D residue  400 HIS
Chi-restraints excluded: chain D residue  610 THR
Chi-restraints excluded: chain D residue  674 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 144 optimal weight:    1.9990
   chunk 169 optimal weight:    4.9990
   chunk 49 optimal weight:    8.9990
   chunk 23 optimal weight:    3.9990
   chunk 75 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 7 optimal weight:    4.9990
   chunk 154 optimal weight:    9.9990
   chunk 93 optimal weight:    5.9990
   chunk 81 optimal weight:    3.9990
   chunk 74 optimal weight:    0.7980
   overall best weight:    2.1386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.162474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.124976 restraints weight = 21232.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.124134 restraints weight = 16383.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.125378 restraints weight = 12263.121|
|-----------------------------------------------------------------------------|
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.2492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  15812  Z= 0.163
  Angle     :  0.558   7.227  21356  Z= 0.290
  Chirality :  0.040   0.123   2328
  Planarity :  0.004   0.044   2684
  Dihedral  :  4.882  50.063   2088
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 16.94 %
    Favored  : 80.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.20), residues: 1860
  helix:  1.65 (0.16), residues: 1184
  sheet: -0.53 (0.39), residues: 132
  loop : -1.49 (0.26), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 451 
 HIS   0.003   0.001   HIS C 257 
 PHE   0.020   0.002   PHE B 343 
 TYR   0.012   0.001   TYR C 468 
 ARG   0.005   0.000   ARG C 391 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05198 (  932)
  hydrogen bonds       : angle       4.06786 ( 2712)
  covalent geometry    : bond        0.00377 (15812)
  covalent geometry    : angle       0.55811 (21356)

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

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

  3720 Ramachandran restraints generated.
    1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3720 Ramachandran restraints generated.
    1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 234
  time to evaluate  : 1.683 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 ASP cc_start: 0.8455 (m-30) cc_final: 0.8202 (m-30)
REVERT: B  267 ASP cc_start: 0.8569 (m-30) cc_final: 0.8339 (m-30)
REVERT: B  273 LEU cc_start: 0.8714 (tp) cc_final: 0.8500 (tp)
REVERT: B  477 MET cc_start: 0.8295 (ttp) cc_final: 0.8017 (ttp)
REVERT: C  233 ARG cc_start: 0.8216 (tmm-80) cc_final: 0.7980 (ttt180)
REVERT: C  273 LEU cc_start: 0.8716 (tp) cc_final: 0.8494 (tp)
  outliers start: 37
  outliers final: 27
  residues processed: 253
  average time/residue: 0.2764
  time to fit residues: 104.3959
Evaluate side-chains
  245 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 218
  time to evaluate  : 1.768 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  255 ILE
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  293 THR
Chi-restraints excluded: chain A residue  400 HIS
Chi-restraints excluded: chain A residue  610 THR
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  678 THR
Chi-restraints excluded: chain B residue  255 ILE
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  293 THR
Chi-restraints excluded: chain B residue  304 ASP
Chi-restraints excluded: chain B residue  400 HIS
Chi-restraints excluded: chain B residue  610 THR
Chi-restraints excluded: chain B residue  674 VAL
Chi-restraints excluded: chain B residue  678 THR
Chi-restraints excluded: chain C residue  255 ILE
Chi-restraints excluded: chain C residue  272 LEU
Chi-restraints excluded: chain C residue  400 HIS
Chi-restraints excluded: chain C residue  610 THR
Chi-restraints excluded: chain C residue  674 VAL
Chi-restraints excluded: chain C residue  678 THR
Chi-restraints excluded: chain D residue  272 LEU
Chi-restraints excluded: chain D residue  400 HIS
Chi-restraints excluded: chain D residue  610 THR
Chi-restraints excluded: chain D residue  674 VAL
Chi-restraints excluded: chain D residue  678 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 177 optimal weight:    6.9990
   chunk 123 optimal weight:    1.9990
   chunk 109 optimal weight:    0.0010
   chunk 64 optimal weight:    5.9990
   chunk 76 optimal weight:    0.9990
   chunk 47 optimal weight:    0.0070
   chunk 104 optimal weight:    9.9990
   chunk 119 optimal weight:    3.9990
   chunk 61 optimal weight:    3.9990
   chunk 145 optimal weight:    0.8980
   chunk 5 optimal weight:    4.9990
   overall best weight:    0.7808

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.166602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.129557 restraints weight = 21326.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.129530 restraints weight = 13665.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.130488 restraints weight = 10654.164|
|-----------------------------------------------------------------------------|
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.2892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  15812  Z= 0.101
  Angle     :  0.485   6.652  21356  Z= 0.251
  Chirality :  0.037   0.117   2328
  Planarity :  0.004   0.042   2684
  Dihedral  :  4.602  51.197   2088
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 17.29 %
    Favored  : 78.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.20), residues: 1860
  helix:  2.01 (0.16), residues: 1156
  sheet: -0.03 (0.42), residues: 108
  loop : -1.10 (0.25), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 451 
 HIS   0.004   0.001   HIS C 553 
 PHE   0.007   0.001   PHE B 659 
 TYR   0.011   0.001   TYR D 507 
 ARG   0.003   0.000   ARG B 588 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03758 (  932)
  hydrogen bonds       : angle       3.81147 ( 2712)
  covalent geometry    : bond        0.00209 (15812)
  covalent geometry    : angle       0.48533 (21356)

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

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

  3720 Ramachandran restraints generated.
    1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3720 Ramachandran restraints generated.
    1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  301 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 237
  time to evaluate  : 2.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  410 TYR cc_start: 0.8176 (m-80) cc_final: 0.7795 (m-80)
REVERT: B  273 LEU cc_start: 0.8704 (tp) cc_final: 0.8426 (tp)
REVERT: B  410 TYR cc_start: 0.8241 (m-80) cc_final: 0.7854 (m-80)
REVERT: C  273 LEU cc_start: 0.8706 (tp) cc_final: 0.8436 (tp)
REVERT: C  410 TYR cc_start: 0.8212 (m-80) cc_final: 0.7864 (m-80)
REVERT: C  591 VAL cc_start: 0.8336 (OUTLIER) cc_final: 0.8127 (p)
REVERT: D  410 TYR cc_start: 0.8245 (m-80) cc_final: 0.7890 (m-80)
  outliers start: 64
  outliers final: 37
  residues processed: 272
  average time/residue: 0.3118
  time to fit residues: 125.6888
Evaluate side-chains
  250 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 212
  time to evaluate  : 1.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  255 ILE
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  274 MET
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  400 HIS
Chi-restraints excluded: chain A residue  610 THR
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain B residue  255 ILE
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  274 MET
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  400 HIS
Chi-restraints excluded: chain B residue  610 THR
Chi-restraints excluded: chain B residue  674 VAL
Chi-restraints excluded: chain C residue  255 ILE
Chi-restraints excluded: chain C residue  272 LEU
Chi-restraints excluded: chain C residue  274 MET
Chi-restraints excluded: chain C residue  293 THR
Chi-restraints excluded: chain C residue  328 ILE
Chi-restraints excluded: chain C residue  345 VAL
Chi-restraints excluded: chain C residue  400 HIS
Chi-restraints excluded: chain C residue  591 VAL
Chi-restraints excluded: chain C residue  610 THR
Chi-restraints excluded: chain C residue  674 VAL
Chi-restraints excluded: chain D residue  255 ILE
Chi-restraints excluded: chain D residue  272 LEU
Chi-restraints excluded: chain D residue  274 MET
Chi-restraints excluded: chain D residue  280 ILE
Chi-restraints excluded: chain D residue  328 ILE
Chi-restraints excluded: chain D residue  345 VAL
Chi-restraints excluded: chain D residue  400 HIS
Chi-restraints excluded: chain D residue  406 PHE
Chi-restraints excluded: chain D residue  610 THR
Chi-restraints excluded: chain D residue  674 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 36 optimal weight:   10.0000
   chunk 112 optimal weight:    0.0770
   chunk 132 optimal weight:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 157 optimal weight:    4.9990
   chunk 131 optimal weight:    4.9990
   chunk 100 optimal weight:    5.9990
   chunk 156 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 106 optimal weight:    3.9990
   overall best weight:    1.8144

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.162980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.126297 restraints weight = 21418.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.125666 restraints weight = 15302.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.126645 restraints weight = 12064.529|
|-----------------------------------------------------------------------------|
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.3006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  15812  Z= 0.145
  Angle     :  0.528   8.416  21356  Z= 0.273
  Chirality :  0.039   0.123   2328
  Planarity :  0.004   0.040   2684
  Dihedral  :  4.646  51.271   2088
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 16.94 %
    Favored  : 79.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.29 (0.20), residues: 1860
  helix:  1.91 (0.16), residues: 1180
  sheet:  0.03 (0.42), residues: 108
  loop : -1.27 (0.25), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 451 
 HIS   0.002   0.001   HIS D 431 
 PHE   0.009   0.001   PHE D 659 
 TYR   0.011   0.001   TYR A 532 
 ARG   0.004   0.000   ARG A 391 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04850 (  932)
  hydrogen bonds       : angle       3.92116 ( 2712)
  covalent geometry    : bond        0.00333 (15812)
  covalent geometry    : angle       0.52810 (21356)

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

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

  3720 Ramachandran restraints generated.
    1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3720 Ramachandran restraints generated.
    1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 226
  time to evaluate  : 1.564 
Fit side-chains
   revert: symmetry clash
REVERT: A  699 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7519 (mmm)
REVERT: B  233 ARG cc_start: 0.8195 (tmm-80) cc_final: 0.7974 (ttt180)
REVERT: B  273 LEU cc_start: 0.8680 (tp) cc_final: 0.8467 (tp)
REVERT: C  267 ASP cc_start: 0.8526 (m-30) cc_final: 0.8319 (m-30)
REVERT: C  591 VAL cc_start: 0.8442 (OUTLIER) cc_final: 0.8240 (p)
REVERT: D  233 ARG cc_start: 0.8230 (tmm-80) cc_final: 0.8019 (ttt180)
REVERT: D  410 TYR cc_start: 0.8298 (m-80) cc_final: 0.7889 (m-80)
  outliers start: 67
  outliers final: 55
  residues processed: 268
  average time/residue: 0.2637
  time to fit residues: 104.8979
Evaluate side-chains
  277 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 220
  time to evaluate  : 1.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  274 MET
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  400 HIS
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  610 THR
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  678 THR
Chi-restraints excluded: chain A residue  684 SER
Chi-restraints excluded: chain A residue  699 MET
Chi-restraints excluded: chain B residue  255 ILE
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  274 MET
Chi-restraints excluded: chain B residue  304 ASP
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  400 HIS
Chi-restraints excluded: chain B residue  406 PHE
Chi-restraints excluded: chain B residue  454 LEU
Chi-restraints excluded: chain B residue  511 ILE
Chi-restraints excluded: chain B residue  610 THR
Chi-restraints excluded: chain B residue  674 VAL
Chi-restraints excluded: chain B residue  678 THR
Chi-restraints excluded: chain B residue  684 SER
Chi-restraints excluded: chain C residue  255 ILE
Chi-restraints excluded: chain C residue  272 LEU
Chi-restraints excluded: chain C residue  274 MET
Chi-restraints excluded: chain C residue  293 THR
Chi-restraints excluded: chain C residue  328 ILE
Chi-restraints excluded: chain C residue  345 VAL
Chi-restraints excluded: chain C residue  392 LEU
Chi-restraints excluded: chain C residue  400 HIS
Chi-restraints excluded: chain C residue  406 PHE
Chi-restraints excluded: chain C residue  454 LEU
Chi-restraints excluded: chain C residue  511 ILE
Chi-restraints excluded: chain C residue  591 VAL
Chi-restraints excluded: chain C residue  610 THR
Chi-restraints excluded: chain C residue  674 VAL
Chi-restraints excluded: chain C residue  678 THR
Chi-restraints excluded: chain C residue  684 SER
Chi-restraints excluded: chain D residue  255 ILE
Chi-restraints excluded: chain D residue  272 LEU
Chi-restraints excluded: chain D residue  274 MET
Chi-restraints excluded: chain D residue  280 ILE
Chi-restraints excluded: chain D residue  304 ASP
Chi-restraints excluded: chain D residue  345 VAL
Chi-restraints excluded: chain D residue  392 LEU
Chi-restraints excluded: chain D residue  400 HIS
Chi-restraints excluded: chain D residue  454 LEU
Chi-restraints excluded: chain D residue  610 THR
Chi-restraints excluded: chain D residue  674 VAL
Chi-restraints excluded: chain D residue  678 THR
Chi-restraints excluded: chain D residue  684 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 178 optimal weight:    8.9990
   chunk 123 optimal weight:    1.9990
   chunk 136 optimal weight:    3.9990
   chunk 133 optimal weight:    7.9990
   chunk 128 optimal weight:    3.9990
   chunk 153 optimal weight:    0.0870
   chunk 172 optimal weight:    4.9990
   chunk 146 optimal weight:    3.9990
   chunk 61 optimal weight:    6.9990
   chunk 139 optimal weight:   10.0000
   chunk 16 optimal weight:    9.9990
   overall best weight:    2.8166

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

Flipped N/Q/H residues before XYZ refinement:
A 324 ASN
B 324 ASN
C 324 ASN
D 324 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.160182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.124858 restraints weight = 21587.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.122494 restraints weight = 14207.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.123875 restraints weight = 12564.416|
|-----------------------------------------------------------------------------|
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.3111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057  15812  Z= 0.199
  Angle     :  0.571   7.205  21356  Z= 0.299
  Chirality :  0.041   0.127   2328
  Planarity :  0.004   0.038   2684
  Dihedral  :  4.856  51.962   2088
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 17.00 %
    Favored  : 78.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.08 (0.20), residues: 1860
  helix:  1.66 (0.16), residues: 1192
  sheet: -0.06 (0.42), residues: 108
  loop : -1.20 (0.25), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C 451 
 HIS   0.003   0.001   HIS C 257 
 PHE   0.012   0.002   PHE D 471 
 TYR   0.012   0.001   TYR C 468 
 ARG   0.004   0.000   ARG C 391 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05565 (  932)
  hydrogen bonds       : angle       4.12262 ( 2712)
  covalent geometry    : bond        0.00471 (15812)
  covalent geometry    : angle       0.57117 (21356)

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

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

  3720 Ramachandran restraints generated.
    1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3720 Ramachandran restraints generated.
    1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 78
    poor density    : 232
  time to evaluate  : 1.573 
Fit side-chains
REVERT: B  233 ARG cc_start: 0.8177 (tmm-80) cc_final: 0.7916 (ttt180)
REVERT: B  273 LEU cc_start: 0.8659 (tp) cc_final: 0.8382 (tp)
REVERT: C  273 LEU cc_start: 0.8678 (tp) cc_final: 0.8187 (tt)
REVERT: D  233 ARG cc_start: 0.8209 (tmm-80) cc_final: 0.7933 (ttt180)
  outliers start: 78
  outliers final: 55
  residues processed: 281
  average time/residue: 0.2969
  time to fit residues: 127.5501
Evaluate side-chains
  276 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 221
  time to evaluate  : 1.945 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  255 ILE
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  274 MET
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  304 ASP
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  400 HIS
Chi-restraints excluded: chain A residue  406 PHE
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  610 THR
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  678 THR
Chi-restraints excluded: chain A residue  684 SER
Chi-restraints excluded: chain B residue  255 ILE
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  274 MET
Chi-restraints excluded: chain B residue  293 THR
Chi-restraints excluded: chain B residue  304 ASP
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  400 HIS
Chi-restraints excluded: chain B residue  406 PHE
Chi-restraints excluded: chain B residue  454 LEU
Chi-restraints excluded: chain B residue  610 THR
Chi-restraints excluded: chain B residue  674 VAL
Chi-restraints excluded: chain B residue  678 THR
Chi-restraints excluded: chain B residue  684 SER
Chi-restraints excluded: chain C residue  255 ILE
Chi-restraints excluded: chain C residue  272 LEU
Chi-restraints excluded: chain C residue  274 MET
Chi-restraints excluded: chain C residue  280 ILE
Chi-restraints excluded: chain C residue  293 THR
Chi-restraints excluded: chain C residue  304 ASP
Chi-restraints excluded: chain C residue  345 VAL
Chi-restraints excluded: chain C residue  400 HIS
Chi-restraints excluded: chain C residue  406 PHE
Chi-restraints excluded: chain C residue  454 LEU
Chi-restraints excluded: chain C residue  610 THR
Chi-restraints excluded: chain C residue  674 VAL
Chi-restraints excluded: chain C residue  678 THR
Chi-restraints excluded: chain C residue  684 SER
Chi-restraints excluded: chain D residue  255 ILE
Chi-restraints excluded: chain D residue  272 LEU
Chi-restraints excluded: chain D residue  274 MET
Chi-restraints excluded: chain D residue  280 ILE
Chi-restraints excluded: chain D residue  304 ASP
Chi-restraints excluded: chain D residue  328 ILE
Chi-restraints excluded: chain D residue  345 VAL
Chi-restraints excluded: chain D residue  400 HIS
Chi-restraints excluded: chain D residue  406 PHE
Chi-restraints excluded: chain D residue  454 LEU
Chi-restraints excluded: chain D residue  610 THR
Chi-restraints excluded: chain D residue  640 VAL
Chi-restraints excluded: chain D residue  674 VAL
Chi-restraints excluded: chain D residue  678 THR
Chi-restraints excluded: chain D residue  684 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 160 optimal weight:    6.9990
   chunk 70 optimal weight:    2.9990
   chunk 79 optimal weight:    1.9990
   chunk 149 optimal weight:   10.0000
   chunk 169 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 148 optimal weight:   10.0000
   chunk 166 optimal weight:    0.7980
   chunk 175 optimal weight:    3.9990
   chunk 171 optimal weight:    0.9990
   chunk 78 optimal weight:    2.9990
   overall best weight:    1.3386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.163806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.128141 restraints weight = 21654.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.126663 restraints weight = 14070.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.127754 restraints weight = 12115.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.3302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  15812  Z= 0.123
  Angle     :  0.506   7.588  21356  Z= 0.263
  Chirality :  0.038   0.121   2328
  Planarity :  0.004   0.039   2684
  Dihedral  :  4.629  52.323   2088
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 17.65 %
    Favored  : 79.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.54 (0.20), residues: 1860
  helix:  2.00 (0.16), residues: 1172
  sheet:  0.09 (0.43), residues: 108
  loop : -0.83 (0.26), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 451 
 HIS   0.003   0.001   HIS C 553 
 PHE   0.009   0.001   PHE D 659 
 TYR   0.020   0.001   TYR C 507 
 ARG   0.006   0.000   ARG A 588 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04268 (  932)
  hydrogen bonds       : angle       3.92189 ( 2712)
  covalent geometry    : bond        0.00280 (15812)
  covalent geometry    : angle       0.50622 (21356)

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

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

  3720 Ramachandran restraints generated.
    1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3720 Ramachandran restraints generated.
    1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  294 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 239
  time to evaluate  : 1.633 
Fit side-chains
REVERT: B  273 LEU cc_start: 0.8623 (tp) cc_final: 0.8371 (tp)
REVERT: C  273 LEU cc_start: 0.8620 (tp) cc_final: 0.8371 (tp)
REVERT: D  233 ARG cc_start: 0.8226 (tmm-80) cc_final: 0.8026 (ttp80)
REVERT: D  273 LEU cc_start: 0.8649 (tp) cc_final: 0.8185 (tt)
  outliers start: 55
  outliers final: 52
  residues processed: 274
  average time/residue: 0.3290
  time to fit residues: 135.9400
Evaluate side-chains
  284 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 232
  time to evaluate  : 1.706 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  255 ILE
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  274 MET
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  293 THR
Chi-restraints excluded: chain A residue  304 ASP
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  400 HIS
Chi-restraints excluded: chain A residue  406 PHE
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  610 THR
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  678 THR
Chi-restraints excluded: chain B residue  255 ILE
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  274 MET
Chi-restraints excluded: chain B residue  304 ASP
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  400 HIS
Chi-restraints excluded: chain B residue  406 PHE
Chi-restraints excluded: chain B residue  454 LEU
Chi-restraints excluded: chain B residue  610 THR
Chi-restraints excluded: chain B residue  674 VAL
Chi-restraints excluded: chain B residue  684 SER
Chi-restraints excluded: chain C residue  255 ILE
Chi-restraints excluded: chain C residue  272 LEU
Chi-restraints excluded: chain C residue  274 MET
Chi-restraints excluded: chain C residue  293 THR
Chi-restraints excluded: chain C residue  304 ASP
Chi-restraints excluded: chain C residue  328 ILE
Chi-restraints excluded: chain C residue  345 VAL
Chi-restraints excluded: chain C residue  400 HIS
Chi-restraints excluded: chain C residue  406 PHE
Chi-restraints excluded: chain C residue  454 LEU
Chi-restraints excluded: chain C residue  610 THR
Chi-restraints excluded: chain C residue  674 VAL
Chi-restraints excluded: chain C residue  678 THR
Chi-restraints excluded: chain C residue  684 SER
Chi-restraints excluded: chain D residue  255 ILE
Chi-restraints excluded: chain D residue  272 LEU
Chi-restraints excluded: chain D residue  274 MET
Chi-restraints excluded: chain D residue  280 ILE
Chi-restraints excluded: chain D residue  304 ASP
Chi-restraints excluded: chain D residue  328 ILE
Chi-restraints excluded: chain D residue  345 VAL
Chi-restraints excluded: chain D residue  400 HIS
Chi-restraints excluded: chain D residue  406 PHE
Chi-restraints excluded: chain D residue  454 LEU
Chi-restraints excluded: chain D residue  610 THR
Chi-restraints excluded: chain D residue  674 VAL
Chi-restraints excluded: chain D residue  684 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 95 optimal weight:   10.0000
   chunk 40 optimal weight:    2.9990
   chunk 107 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 1 optimal weight:    9.9990
   chunk 53 optimal weight:    1.9990
   chunk 142 optimal weight:    0.9990
   chunk 97 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   chunk 155 optimal weight:    5.9990
   chunk 153 optimal weight:    0.8980
   overall best weight:    1.5788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.163202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.127512 restraints weight = 21379.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.126097 restraints weight = 14293.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.127236 restraints weight = 11870.366|
|-----------------------------------------------------------------------------|
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.3383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  15812  Z= 0.135
  Angle     :  0.510   6.429  21356  Z= 0.267
  Chirality :  0.039   0.121   2328
  Planarity :  0.004   0.039   2684
  Dihedral  :  4.601  51.902   2088
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 16.94 %
    Favored  : 79.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.62 (0.20), residues: 1860
  helix:  2.03 (0.16), residues: 1172
  sheet:  0.17 (0.43), residues: 108
  loop : -0.74 (0.26), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 451 
 HIS   0.002   0.001   HIS C 553 
 PHE   0.009   0.001   PHE A 659 
 TYR   0.023   0.001   TYR B 507 
 ARG   0.006   0.000   ARG D 588 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04506 (  932)
  hydrogen bonds       : angle       3.94658 ( 2712)
  covalent geometry    : bond        0.00312 (15812)
  covalent geometry    : angle       0.50970 (21356)

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

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

  3720 Ramachandran restraints generated.
    1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3720 Ramachandran restraints generated.
    1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  303 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 241
  time to evaluate  : 1.974 
Fit side-chains
   revert: symmetry clash
REVERT: B  273 LEU cc_start: 0.8630 (tp) cc_final: 0.8371 (tp)
REVERT: B  430 CYS cc_start: 0.8227 (m) cc_final: 0.7967 (m)
REVERT: C  273 LEU cc_start: 0.8623 (tp) cc_final: 0.8346 (tp)
REVERT: D  273 LEU cc_start: 0.8647 (tp) cc_final: 0.8174 (tt)
  outliers start: 62
  outliers final: 51
  residues processed: 283
  average time/residue: 0.2583
  time to fit residues: 110.4887
Evaluate side-chains
  288 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 237
  time to evaluate  : 1.841 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  255 ILE
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  274 MET
Chi-restraints excluded: chain A residue  293 THR
Chi-restraints excluded: chain A residue  304 ASP
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  400 HIS
Chi-restraints excluded: chain A residue  406 PHE
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  610 THR
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  678 THR
Chi-restraints excluded: chain A residue  684 SER
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  274 MET
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  400 HIS
Chi-restraints excluded: chain B residue  454 LEU
Chi-restraints excluded: chain B residue  511 ILE
Chi-restraints excluded: chain B residue  610 THR
Chi-restraints excluded: chain B residue  674 VAL
Chi-restraints excluded: chain B residue  678 THR
Chi-restraints excluded: chain B residue  684 SER
Chi-restraints excluded: chain C residue  272 LEU
Chi-restraints excluded: chain C residue  274 MET
Chi-restraints excluded: chain C residue  293 THR
Chi-restraints excluded: chain C residue  304 ASP
Chi-restraints excluded: chain C residue  328 ILE
Chi-restraints excluded: chain C residue  345 VAL
Chi-restraints excluded: chain C residue  400 HIS
Chi-restraints excluded: chain C residue  406 PHE
Chi-restraints excluded: chain C residue  454 LEU
Chi-restraints excluded: chain C residue  610 THR
Chi-restraints excluded: chain C residue  674 VAL
Chi-restraints excluded: chain C residue  678 THR
Chi-restraints excluded: chain C residue  684 SER
Chi-restraints excluded: chain D residue  255 ILE
Chi-restraints excluded: chain D residue  272 LEU
Chi-restraints excluded: chain D residue  274 MET
Chi-restraints excluded: chain D residue  304 ASP
Chi-restraints excluded: chain D residue  328 ILE
Chi-restraints excluded: chain D residue  345 VAL
Chi-restraints excluded: chain D residue  400 HIS
Chi-restraints excluded: chain D residue  406 PHE
Chi-restraints excluded: chain D residue  454 LEU
Chi-restraints excluded: chain D residue  610 THR
Chi-restraints excluded: chain D residue  674 VAL
Chi-restraints excluded: chain D residue  678 THR
Chi-restraints excluded: chain D residue  684 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 71 optimal weight:    3.9990
   chunk 159 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 130 optimal weight:    2.9990
   chunk 12 optimal weight:    9.9990
   chunk 43 optimal weight:    8.9990
   chunk 90 optimal weight:    0.6980
   chunk 128 optimal weight:    0.0370
   chunk 73 optimal weight:    1.9990
   chunk 131 optimal weight:    7.9990
   chunk 84 optimal weight:    0.5980
   overall best weight:    0.6660

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.168134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.130516 restraints weight = 21322.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.132040 restraints weight = 11536.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.133000 restraints weight = 8814.254|
|-----------------------------------------------------------------------------|
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.3669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  15812  Z= 0.098
  Angle     :  0.479   6.309  21356  Z= 0.248
  Chirality :  0.037   0.118   2328
  Planarity :  0.004   0.040   2684
  Dihedral  :  4.424  51.698   2088
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 18.06 %
    Favored  : 79.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.87 (0.20), residues: 1860
  helix:  2.23 (0.15), residues: 1172
  sheet:  0.33 (0.43), residues: 108
  loop : -0.65 (0.26), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 451 
 HIS   0.004   0.001   HIS C 553 
 PHE   0.007   0.001   PHE D 659 
 TYR   0.010   0.001   TYR C 532 
 ARG   0.007   0.000   ARG B 588 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03461 (  932)
  hydrogen bonds       : angle       3.78484 ( 2712)
  covalent geometry    : bond        0.00207 (15812)
  covalent geometry    : angle       0.47923 (21356)

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

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

  3720 Ramachandran restraints generated.
    1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3720 Ramachandran restraints generated.
    1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  296 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 254
  time to evaluate  : 1.722 
Fit side-chains
   revert: symmetry clash
REVERT: A  410 TYR cc_start: 0.7940 (m-80) cc_final: 0.7458 (m-80)
REVERT: B  230 PHE cc_start: 0.7440 (t80) cc_final: 0.7239 (t80)
REVERT: B  273 LEU cc_start: 0.8496 (tp) cc_final: 0.8256 (tp)
REVERT: B  410 TYR cc_start: 0.8031 (m-80) cc_final: 0.7641 (m-80)
REVERT: B  430 CYS cc_start: 0.8224 (m) cc_final: 0.7764 (m)
REVERT: B  510 PHE cc_start: 0.8914 (t80) cc_final: 0.8643 (t80)
REVERT: B  699 MET cc_start: 0.8015 (mmt) cc_final: 0.7805 (mmt)
REVERT: C  273 LEU cc_start: 0.8513 (tp) cc_final: 0.8269 (tp)
REVERT: C  410 TYR cc_start: 0.7942 (m-80) cc_final: 0.7541 (m-80)
REVERT: C  510 PHE cc_start: 0.8890 (t80) cc_final: 0.8639 (t80)
REVERT: D  230 PHE cc_start: 0.7461 (t80) cc_final: 0.7209 (t80)
REVERT: D  273 LEU cc_start: 0.8559 (tp) cc_final: 0.8304 (tp)
REVERT: D  410 TYR cc_start: 0.8015 (m-80) cc_final: 0.7683 (m-80)
  outliers start: 42
  outliers final: 38
  residues processed: 284
  average time/residue: 0.2525
  time to fit residues: 107.6915
Evaluate side-chains
  282 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 244
  time to evaluate  : 1.713 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  293 THR
Chi-restraints excluded: chain A residue  304 ASP
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  400 HIS
Chi-restraints excluded: chain A residue  406 PHE
Chi-restraints excluded: chain A residue  610 THR
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  678 THR
Chi-restraints excluded: chain A residue  684 SER
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  274 MET
Chi-restraints excluded: chain B residue  293 THR
Chi-restraints excluded: chain B residue  304 ASP
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  400 HIS
Chi-restraints excluded: chain B residue  610 THR
Chi-restraints excluded: chain B residue  674 VAL
Chi-restraints excluded: chain B residue  678 THR
Chi-restraints excluded: chain C residue  272 LEU
Chi-restraints excluded: chain C residue  274 MET
Chi-restraints excluded: chain C residue  293 THR
Chi-restraints excluded: chain C residue  328 ILE
Chi-restraints excluded: chain C residue  345 VAL
Chi-restraints excluded: chain C residue  400 HIS
Chi-restraints excluded: chain C residue  610 THR
Chi-restraints excluded: chain C residue  674 VAL
Chi-restraints excluded: chain C residue  678 THR
Chi-restraints excluded: chain D residue  272 LEU
Chi-restraints excluded: chain D residue  274 MET
Chi-restraints excluded: chain D residue  328 ILE
Chi-restraints excluded: chain D residue  345 VAL
Chi-restraints excluded: chain D residue  400 HIS
Chi-restraints excluded: chain D residue  610 THR
Chi-restraints excluded: chain D residue  674 VAL
Chi-restraints excluded: chain D residue  678 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 152 optimal weight:    0.9990
   chunk 41 optimal weight:    7.9990
   chunk 72 optimal weight:    0.8980
   chunk 36 optimal weight:    4.9990
   chunk 98 optimal weight:    2.9990
   chunk 179 optimal weight:   10.0000
   chunk 24 optimal weight:    0.9980
   chunk 37 optimal weight:    0.7980
   chunk 128 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 123 optimal weight:    2.9990
   overall best weight:    0.9382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.166686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.130658 restraints weight = 21704.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.131091 restraints weight = 13871.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.131742 restraints weight = 10593.750|
|-----------------------------------------------------------------------------|
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.3720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045  15812  Z= 0.108
  Angle     :  0.495   6.014  21356  Z= 0.254
  Chirality :  0.038   0.127   2328
  Planarity :  0.004   0.041   2684
  Dihedral  :  4.398  51.306   2088
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 18.47 %
    Favored  : 78.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.97 (0.20), residues: 1860
  helix:  2.26 (0.15), residues: 1172
  sheet:  0.50 (0.43), residues: 108
  loop : -0.54 (0.26), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 451 
 HIS   0.003   0.001   HIS C 553 
 PHE   0.008   0.001   PHE D 659 
 TYR   0.009   0.001   TYR A 532 
 ARG   0.007   0.000   ARG C 588 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03829 (  932)
  hydrogen bonds       : angle       3.79158 ( 2712)
  covalent geometry    : bond        0.00236 (15812)
  covalent geometry    : angle       0.49507 (21356)

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

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

  3720 Ramachandran restraints generated.
    1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3720 Ramachandran restraints generated.
    1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 253
  time to evaluate  : 1.639 
Fit side-chains
REVERT: A  410 TYR cc_start: 0.7881 (m-80) cc_final: 0.7423 (m-80)
REVERT: A  510 PHE cc_start: 0.8925 (t80) cc_final: 0.8616 (t80)
REVERT: B  273 LEU cc_start: 0.8567 (tp) cc_final: 0.8327 (tp)
REVERT: B  410 TYR cc_start: 0.8014 (m-80) cc_final: 0.7629 (m-80)
REVERT: B  510 PHE cc_start: 0.8965 (t80) cc_final: 0.8644 (t80)
REVERT: C  273 LEU cc_start: 0.8572 (tp) cc_final: 0.8329 (tp)
REVERT: C  410 TYR cc_start: 0.7921 (m-80) cc_final: 0.7470 (m-80)
REVERT: D  273 LEU cc_start: 0.8604 (tp) cc_final: 0.8372 (tp)
REVERT: D  410 TYR cc_start: 0.7987 (m-80) cc_final: 0.7663 (m-80)
  outliers start: 44
  outliers final: 39
  residues processed: 281
  average time/residue: 0.2568
  time to fit residues: 108.2905
Evaluate side-chains
  285 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 246
  time to evaluate  : 1.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  274 MET
Chi-restraints excluded: chain A residue  293 THR
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  400 HIS
Chi-restraints excluded: chain A residue  406 PHE
Chi-restraints excluded: chain A residue  610 THR
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  678 THR
Chi-restraints excluded: chain A residue  684 SER
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  274 MET
Chi-restraints excluded: chain B residue  293 THR
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  400 HIS
Chi-restraints excluded: chain B residue  610 THR
Chi-restraints excluded: chain B residue  674 VAL
Chi-restraints excluded: chain B residue  678 THR
Chi-restraints excluded: chain C residue  272 LEU
Chi-restraints excluded: chain C residue  274 MET
Chi-restraints excluded: chain C residue  293 THR
Chi-restraints excluded: chain C residue  328 ILE
Chi-restraints excluded: chain C residue  345 VAL
Chi-restraints excluded: chain C residue  400 HIS
Chi-restraints excluded: chain C residue  454 LEU
Chi-restraints excluded: chain C residue  610 THR
Chi-restraints excluded: chain C residue  674 VAL
Chi-restraints excluded: chain C residue  678 THR
Chi-restraints excluded: chain D residue  272 LEU
Chi-restraints excluded: chain D residue  274 MET
Chi-restraints excluded: chain D residue  328 ILE
Chi-restraints excluded: chain D residue  345 VAL
Chi-restraints excluded: chain D residue  400 HIS
Chi-restraints excluded: chain D residue  474 MET
Chi-restraints excluded: chain D residue  610 THR
Chi-restraints excluded: chain D residue  674 VAL
Chi-restraints excluded: chain D residue  678 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 165 optimal weight:    3.9990
   chunk 123 optimal weight:    2.9990
   chunk 93 optimal weight:    8.9990
   chunk 29 optimal weight:    2.9990
   chunk 79 optimal weight:    0.8980
   chunk 89 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9990
   chunk 137 optimal weight:   10.0000
   chunk 95 optimal weight:   10.0000
   chunk 12 optimal weight:    2.9990
   chunk 45 optimal weight:   10.0000
   overall best weight:    1.7386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.163712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.127924 restraints weight = 21474.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.127152 restraints weight = 14149.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.128053 restraints weight = 11705.108|
|-----------------------------------------------------------------------------|
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.3615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  15812  Z= 0.145
  Angle     :  0.535   6.875  21356  Z= 0.276
  Chirality :  0.039   0.134   2328
  Planarity :  0.004   0.040   2684
  Dihedral  :  4.517  50.917   2088
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 18.47 %
    Favored  : 78.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.90 (0.20), residues: 1860
  helix:  2.21 (0.15), residues: 1172
  sheet:  0.49 (0.44), residues: 108
  loop : -0.58 (0.26), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 494 
 HIS   0.002   0.001   HIS C 553 
 PHE   0.009   0.001   PHE C 659 
 TYR   0.010   0.001   TYR B 468 
 ARG   0.006   0.000   ARG B 588 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04578 (  932)
  hydrogen bonds       : angle       3.93151 ( 2712)
  covalent geometry    : bond        0.00338 (15812)
  covalent geometry    : angle       0.53537 (21356)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4495.65 seconds
wall clock time: 81 minutes 10.85 seconds (4870.85 seconds total)