Starting phenix.real_space_refine
on Fri Jun 13 18:42:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iwo_35775/06_2025/8iwo_35775.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iwo_35775/06_2025/8iwo_35775.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.09
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8iwo_35775/06_2025/8iwo_35775.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iwo_35775/06_2025/8iwo_35775.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iwo_35775/06_2025/8iwo_35775.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iwo_35775/06_2025/8iwo_35775.cif"
  }
  resolution = 3.09
  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=  -0.001 sd=   0.104
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      70      5.16       5
     C    9826      2.51       5
     N    2516      2.21       5
     O    2704      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 48 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 15118
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7516
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 956, 7516
          Classifications: {'peptide': 956}
          Link IDs: {'PTRANS': 32, 'TRANS': 923}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'46E': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 17.62, per 1000 atoms: 1.17
  Number of scatterers: 15118
  At special positions: 0
  Unit cell: (107.06, 100.7, 133.56, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      70     16.00
     P       2     15.00
     O    2704      8.00
     N    2516      7.00
     C    9826      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 4.31
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  3792 Ramachandran restraints generated.
    1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3556

  Finding SS restraints...
    Secondary structure from input PDB file:
      78 helices and 8 sheets defined
      69.5% alpha, 5.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.72
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 29
      removed outlier: 4.098A  pdb=" N   VAL A  12 " --> pdb=" O   PRO A   8 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   LEU A  13 " --> pdb=" O   ASP A   9 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 36 through 54
      removed outlier: 3.658A  pdb=" N   THR A  54 " --> pdb=" O   LEU A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 70
      removed outlier: 3.571A  pdb=" N   ILE A  67 " --> pdb=" O   ALA A  63 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   TRP A  68 " --> pdb=" O   GLY A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 91
      removed outlier: 4.003A  pdb=" N   LEU A  77 " --> pdb=" O   PRO A  73 " (cutoff:3.500A)
      Proline residue:  A  82  - end of helix
      removed outlier: 4.180A  pdb=" N   GLU A  87 " --> pdb=" O   ALA A  83 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   SER A  88 " --> pdb=" O   LEU A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 127
      removed outlier: 3.775A  pdb=" N   ILE A  97 " --> pdb=" O   GLU A  93 " (cutoff:3.500A)
      removed outlier: 5.298A  pdb=" N   ALA A 102 " --> pdb=" O   LYS A  98 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   GLN A 103 " --> pdb=" O   LYS A  99 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   MET A 104 " --> pdb=" O   CYS A 100 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   LEU A 106 " --> pdb=" O   ALA A 102 " (cutoff:3.500A)
      Proline residue:  A 110  - end of helix
    Processing helix  chain 'A' and resid 134 through 143
    Processing helix  chain 'A' and resid 149 through 157
    Processing helix  chain 'A' and resid 161 through 191
      removed outlier: 3.633A  pdb=" N   LEU A 173 " --> pdb=" O   GLU A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 227
    Processing helix  chain 'A' and resid 232 through 254
      removed outlier: 3.900A  pdb=" N   GLU A 236 " --> pdb=" O   ASP A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 273
      removed outlier: 3.708A  pdb=" N   THR A 262 " --> pdb=" O   SER A 258 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   PHE A 273 " --> pdb=" O   PHE A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 278
    Processing helix  chain 'A' and resid 282 through 317
    Processing helix  chain 'A' and resid 324 through 353
      removed outlier: 4.128A  pdb=" N   LEU A 331 " --> pdb=" O   TRP A 327 " (cutoff:3.500A)
      Proline residue:  A 350  - end of helix
    Processing helix  chain 'A' and resid 361 through 370
      removed outlier: 4.121A  pdb=" N   LEU A 367 " --> pdb=" O   GLU A 363 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   TRP A 369 " --> pdb=" O   THR A 365 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ALA A 370 " --> pdb=" O   ILE A 366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 390
      removed outlier: 3.784A  pdb=" N   LEU A 378 " --> pdb=" O   GLY A 374 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   ALA A 390 " --> pdb=" O   ARG A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 430
      removed outlier: 3.661A  pdb=" N   SER A 420 " --> pdb=" O   ILE A 416 " (cutoff:3.500A)
      removed outlier: 4.911A  pdb=" N   GLN A 423 " --> pdb=" O   GLY A 419 " (cutoff:3.500A)
      removed outlier: 4.506A  pdb=" N   PHE A 424 " --> pdb=" O   SER A 420 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LEU A 425 " --> pdb=" O   THR A 421 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   GLY A 430 " --> pdb=" O   LEU A 426 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 460
    Processing helix  chain 'A' and resid 471 through 477
    Processing helix  chain 'A' and resid 479 through 483
      removed outlier: 3.840A  pdb=" N   LEU A 482 " --> pdb=" O   ILE A 479 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 528
      removed outlier: 3.730A  pdb=" N   ARG A 511 " --> pdb=" O   LEU A 507 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   VAL A 512 " --> pdb=" O   ARG A 508 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   LEU A 515 " --> pdb=" O   ARG A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 532 through 547
    Processing helix  chain 'A' and resid 557 through 563
      removed outlier: 4.271A  pdb=" N   LEU A 561 " --> pdb=" O   ASP A 557 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   SER A 563 " --> pdb=" O   LYS A 559 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 569 through 576
      removed outlier: 4.170A  pdb=" N   PHE A 573 " --> pdb=" O   ASN A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 580 through 618
      removed outlier: 3.664A  pdb=" N   THR A 588 " --> pdb=" O   ILE A 584 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   GLU A 593 " --> pdb=" O   VAL A 589 " (cutoff:3.500A)
      removed outlier: 5.242A  pdb=" N   SER A 594 " --> pdb=" O   GLU A 590 " (cutoff:3.500A)
      removed outlier: 4.756A  pdb=" N   GLY A 595 " --> pdb=" O   ARG A 591 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 620 through 634
    Processing helix  chain 'A' and resid 634 through 648
    Processing helix  chain 'A' and resid 650 through 679
      removed outlier: 3.884A  pdb=" N   LYS A 677 " --> pdb=" O   GLN A 673 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   THR A 678 " --> pdb=" O   ASN A 674 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   GLY A 679 " --> pdb=" O   LEU A 675 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 682 through 703
    Processing helix  chain 'A' and resid 711 through 719
      removed outlier: 3.845A  pdb=" N   ASN A 717 " --> pdb=" O   SER A 713 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 719 through 724
    Processing helix  chain 'A' and resid 730 through 735
    Processing helix  chain 'A' and resid 790 through 797
      removed outlier: 3.505A  pdb=" N   VAL A 794 " --> pdb=" O   GLY A 790 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 817 through 827
      removed outlier: 3.927A  pdb=" N   ASP A 827 " --> pdb=" O   LEU A 823 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 828 through 847
      removed outlier: 4.276A  pdb=" N   ILE A 832 " --> pdb=" O   PRO A 828 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   PHE A 833 " --> pdb=" O   SER A 829 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   LEU A 834 " --> pdb=" O   ILE A 830 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   LEU A 840 " --> pdb=" O   GLN A 836 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   VAL A 841 " --> pdb=" O   GLU A 837 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 855 through 865
    Processing helix  chain 'A' and resid 913 through 917
    Processing helix  chain 'A' and resid 979 through 983
      removed outlier: 3.828A  pdb=" N   LEU A 983 " --> pdb=" O   SER A 980 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1010 through 1021
    Processing helix  chain 'B' and resid 8 through 29
      removed outlier: 4.098A  pdb=" N   VAL B  12 " --> pdb=" O   PRO B   8 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   LEU B  13 " --> pdb=" O   ASP B   9 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 36 through 54
      removed outlier: 3.659A  pdb=" N   THR B  54 " --> pdb=" O   LEU B  50 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 70
      removed outlier: 3.571A  pdb=" N   ILE B  67 " --> pdb=" O   ALA B  63 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   TRP B  68 " --> pdb=" O   GLY B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 72 through 91
      removed outlier: 4.003A  pdb=" N   LEU B  77 " --> pdb=" O   PRO B  73 " (cutoff:3.500A)
      Proline residue:  B  82  - end of helix
      removed outlier: 4.180A  pdb=" N   GLU B  87 " --> pdb=" O   ALA B  83 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   SER B  88 " --> pdb=" O   LEU B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 127
      removed outlier: 3.775A  pdb=" N   ILE B  97 " --> pdb=" O   GLU B  93 " (cutoff:3.500A)
      removed outlier: 5.298A  pdb=" N   ALA B 102 " --> pdb=" O   LYS B  98 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   GLN B 103 " --> pdb=" O   LYS B  99 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   MET B 104 " --> pdb=" O   CYS B 100 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   LEU B 106 " --> pdb=" O   ALA B 102 " (cutoff:3.500A)
      Proline residue:  B 110  - end of helix
    Processing helix  chain 'B' and resid 134 through 143
    Processing helix  chain 'B' and resid 149 through 157
    Processing helix  chain 'B' and resid 161 through 191
      removed outlier: 3.634A  pdb=" N   LEU B 173 " --> pdb=" O   GLU B 169 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 196 through 227
    Processing helix  chain 'B' and resid 232 through 254
      removed outlier: 3.901A  pdb=" N   GLU B 236 " --> pdb=" O   ASP B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 258 through 273
      removed outlier: 3.707A  pdb=" N   THR B 262 " --> pdb=" O   SER B 258 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   PHE B 273 " --> pdb=" O   PHE B 269 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 273 through 278
    Processing helix  chain 'B' and resid 282 through 317
    Processing helix  chain 'B' and resid 324 through 353
      removed outlier: 4.128A  pdb=" N   LEU B 331 " --> pdb=" O   TRP B 327 " (cutoff:3.500A)
      Proline residue:  B 350  - end of helix
    Processing helix  chain 'B' and resid 361 through 370
      removed outlier: 4.122A  pdb=" N   LEU B 367 " --> pdb=" O   GLU B 363 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   TRP B 369 " --> pdb=" O   THR B 365 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ALA B 370 " --> pdb=" O   ILE B 366 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 374 through 390
      removed outlier: 3.784A  pdb=" N   LEU B 378 " --> pdb=" O   GLY B 374 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   ALA B 390 " --> pdb=" O   ARG B 386 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 396 through 430
      removed outlier: 3.661A  pdb=" N   SER B 420 " --> pdb=" O   ILE B 416 " (cutoff:3.500A)
      removed outlier: 4.911A  pdb=" N   GLN B 423 " --> pdb=" O   GLY B 419 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   PHE B 424 " --> pdb=" O   SER B 420 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LEU B 425 " --> pdb=" O   THR B 421 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   GLY B 430 " --> pdb=" O   LEU B 426 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 438 through 460
    Processing helix  chain 'B' and resid 471 through 477
    Processing helix  chain 'B' and resid 479 through 483
      removed outlier: 3.840A  pdb=" N   LEU B 482 " --> pdb=" O   ILE B 479 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 528
      removed outlier: 3.730A  pdb=" N   ARG B 511 " --> pdb=" O   LEU B 507 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   VAL B 512 " --> pdb=" O   ARG B 508 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   LEU B 515 " --> pdb=" O   ARG B 511 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 532 through 547
    Processing helix  chain 'B' and resid 557 through 563
      removed outlier: 4.271A  pdb=" N   LEU B 561 " --> pdb=" O   ASP B 557 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   SER B 563 " --> pdb=" O   LYS B 559 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 569 through 576
      removed outlier: 4.170A  pdb=" N   PHE B 573 " --> pdb=" O   ASN B 569 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 580 through 618
      removed outlier: 3.664A  pdb=" N   THR B 588 " --> pdb=" O   ILE B 584 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   GLU B 593 " --> pdb=" O   VAL B 589 " (cutoff:3.500A)
      removed outlier: 5.242A  pdb=" N   SER B 594 " --> pdb=" O   GLU B 590 " (cutoff:3.500A)
      removed outlier: 4.755A  pdb=" N   GLY B 595 " --> pdb=" O   ARG B 591 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 620 through 634
    Processing helix  chain 'B' and resid 634 through 648
    Processing helix  chain 'B' and resid 650 through 679
      removed outlier: 3.884A  pdb=" N   LYS B 677 " --> pdb=" O   GLN B 673 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   THR B 678 " --> pdb=" O   ASN B 674 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   GLY B 679 " --> pdb=" O   LEU B 675 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 682 through 703
    Processing helix  chain 'B' and resid 711 through 719
      removed outlier: 3.845A  pdb=" N   ASN B 717 " --> pdb=" O   SER B 713 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 719 through 724
    Processing helix  chain 'B' and resid 730 through 735
    Processing helix  chain 'B' and resid 790 through 797
      removed outlier: 3.505A  pdb=" N   VAL B 794 " --> pdb=" O   GLY B 790 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 817 through 827
      removed outlier: 3.927A  pdb=" N   ASP B 827 " --> pdb=" O   LEU B 823 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 828 through 847
      removed outlier: 4.276A  pdb=" N   ILE B 832 " --> pdb=" O   PRO B 828 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   PHE B 833 " --> pdb=" O   SER B 829 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   LEU B 834 " --> pdb=" O   ILE B 830 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   LEU B 840 " --> pdb=" O   GLN B 836 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   VAL B 841 " --> pdb=" O   GLU B 837 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 855 through 865
    Processing helix  chain 'B' and resid 913 through 917
    Processing helix  chain 'B' and resid 979 through 983
      removed outlier: 3.828A  pdb=" N   LEU B 983 " --> pdb=" O   SER B 980 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1010 through 1021
    Processing sheet with id=AA1, first strand: chain 'A' and resid 740 through 742
      removed outlier: 3.620A  pdb=" N   ILE A 763 " --> pdb=" O   HIS A 811 " (cutoff:3.500A)
      removed outlier: 7.294A  pdb=" N   PHE A 813 " --> pdb=" O   VAL A 761 " (cutoff:3.500A)
      removed outlier: 5.470A  pdb=" N   VAL A 761 " --> pdb=" O   PHE A 813 " (cutoff:3.500A)
      removed outlier: 7.319A  pdb=" N   ILE A 815 " --> pdb=" O   TRP A 759 " (cutoff:3.500A)
      removed outlier: 5.832A  pdb=" N   TRP A 759 " --> pdb=" O   ILE A 815 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 747 through 749
      removed outlier: 7.010A  pdb=" N   MET A 804 " --> pdb=" O   LEU A 748 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 868 through 872
      removed outlier: 6.854A  pdb=" N   LEU A 945 " --> pdb=" O   LEU A 888 " (cutoff:3.500A)
      removed outlier: 5.644A  pdb=" N   LEU A 888 " --> pdb=" O   LEU A 945 " (cutoff:3.500A)
      removed outlier: 7.179A  pdb=" N   VAL A 947 " --> pdb=" O   GLY A 886 " (cutoff:3.500A)
      removed outlier: 5.442A  pdb=" N   GLY A 886 " --> pdb=" O   VAL A 947 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   LEU A 906 " --> pdb=" O   TYR A 931 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 877 through 878
    Processing sheet with id=AA5, first strand: chain 'B' and resid 740 through 742
      removed outlier: 3.620A  pdb=" N   ILE B 763 " --> pdb=" O   HIS B 811 " (cutoff:3.500A)
      removed outlier: 7.294A  pdb=" N   PHE B 813 " --> pdb=" O   VAL B 761 " (cutoff:3.500A)
      removed outlier: 5.470A  pdb=" N   VAL B 761 " --> pdb=" O   PHE B 813 " (cutoff:3.500A)
      removed outlier: 7.320A  pdb=" N   ILE B 815 " --> pdb=" O   TRP B 759 " (cutoff:3.500A)
      removed outlier: 5.832A  pdb=" N   TRP B 759 " --> pdb=" O   ILE B 815 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 747 through 749
      removed outlier: 7.010A  pdb=" N   MET B 804 " --> pdb=" O   LEU B 748 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 868 through 872
      removed outlier: 6.855A  pdb=" N   LEU B 945 " --> pdb=" O   LEU B 888 " (cutoff:3.500A)
      removed outlier: 5.643A  pdb=" N   LEU B 888 " --> pdb=" O   LEU B 945 " (cutoff:3.500A)
      removed outlier: 7.179A  pdb=" N   VAL B 947 " --> pdb=" O   GLY B 886 " (cutoff:3.500A)
      removed outlier: 5.441A  pdb=" N   GLY B 886 " --> pdb=" O   VAL B 947 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   LEU B 906 " --> pdb=" O   TYR B 931 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 877 through 878

    962 hydrogen bonds defined for protein.
    2814 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 5.43

  Time building geometry restraints manager: 4.81 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 2398
        1.30 -     1.43: 3942
        1.43 -     1.56: 8960
        1.56 -     1.69: 4
        1.69 -     1.82: 124
  Bond restraints: 15428
  Sorted by residual:
  bond pdb=" C   ASP A 731 "
       pdb=" O   ASP A 731 "
    ideal  model  delta    sigma   weight residual
    1.241  1.173  0.068 9.80e-03 1.04e+04 4.85e+01
  bond pdb=" C   ASP B 731 "
       pdb=" O   ASP B 731 "
    ideal  model  delta    sigma   weight residual
    1.241  1.173  0.068 9.80e-03 1.04e+04 4.81e+01
  bond pdb=" C   ASN B 418 "
       pdb=" O   ASN B 418 "
    ideal  model  delta    sigma   weight residual
    1.236  1.179  0.058 1.15e-02 7.56e+03 2.54e+01
  bond pdb=" C   ASN A 418 "
       pdb=" O   ASN A 418 "
    ideal  model  delta    sigma   weight residual
    1.236  1.179  0.058 1.15e-02 7.56e+03 2.52e+01
  bond pdb=" C   LEU A 119 "
       pdb=" O   LEU A 119 "
    ideal  model  delta    sigma   weight residual
    1.237  1.181  0.056 1.17e-02 7.31e+03 2.26e+01
  ... (remaining 15423 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.19: 19461
        2.19 -     4.38: 1152
        4.38 -     6.57: 248
        6.57 -     8.76: 29
        8.76 -    10.95: 12
  Bond angle restraints: 20902
  Sorted by residual:
  angle pdb=" N   GLN A 575 "
        pdb=" CA  GLN A 575 "
        pdb=" C   GLN A 575 "
      ideal   model   delta    sigma   weight residual
     111.36  101.41    9.95 1.09e+00 8.42e-01 8.33e+01
  angle pdb=" N   GLN B 575 "
        pdb=" CA  GLN B 575 "
        pdb=" C   GLN B 575 "
      ideal   model   delta    sigma   weight residual
     111.36  101.45    9.91 1.09e+00 8.42e-01 8.27e+01
  angle pdb=" N   GLU B 831 "
        pdb=" CA  GLU B 831 "
        pdb=" C   GLU B 831 "
      ideal   model   delta    sigma   weight residual
     113.12  103.58    9.54 1.25e+00 6.40e-01 5.83e+01
  angle pdb=" N   GLU A 831 "
        pdb=" CA  GLU A 831 "
        pdb=" C   GLU A 831 "
      ideal   model   delta    sigma   weight residual
     113.12  103.58    9.54 1.25e+00 6.40e-01 5.83e+01
  angle pdb=" CA  LEU B 733 "
        pdb=" C   LEU B 733 "
        pdb=" O   LEU B 733 "
      ideal   model   delta    sigma   weight residual
     120.82  113.48    7.34 1.05e+00 9.07e-01 4.89e+01
  ... (remaining 20897 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.33: 8594
       25.33 -    50.67: 534
       50.67 -    76.00: 54
       76.00 -   101.34: 12
      101.34 -   126.67: 2
  Dihedral angle restraints: 9196
    sinusoidal: 3680
      harmonic: 5516
  Sorted by residual:
  dihedral pdb=" C   GLN B 676 "
           pdb=" N   GLN B 676 "
           pdb=" CA  GLN B 676 "
           pdb=" CB  GLN B 676 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -111.81  -10.79     0      2.50e+00 1.60e-01 1.86e+01
  dihedral pdb=" C   GLN A 676 "
           pdb=" N   GLN A 676 "
           pdb=" CA  GLN A 676 "
           pdb=" CB  GLN A 676 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -111.83  -10.77     0      2.50e+00 1.60e-01 1.85e+01
  dihedral pdb=" C37 46E A1201 "
           pdb=" C38 46E A1201 "
           pdb=" C39 46E A1201 "
           pdb=" C3A 46E A1201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     178.43  -54.90 -126.67     1      3.00e+01 1.11e-03 1.70e+01
  ... (remaining 9193 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.075: 2099
       0.075 -    0.149: 237
       0.149 -    0.224: 81
       0.224 -    0.299: 29
       0.299 -    0.374: 6
  Chirality restraints: 2452
  Sorted by residual:
  chirality pdb=" CA  ILE A 815 "
            pdb=" N   ILE A 815 "
            pdb=" C   ILE A 815 "
            pdb=" CB  ILE A 815 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.81   -0.37 2.00e-01 2.50e+01 3.49e+00
  chirality pdb=" CA  ILE B 815 "
            pdb=" N   ILE B 815 "
            pdb=" C   ILE B 815 "
            pdb=" CB  ILE B 815 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.81   -0.37 2.00e-01 2.50e+01 3.48e+00
  chirality pdb=" CA  ILE B 805 "
            pdb=" N   ILE B 805 "
            pdb=" C   ILE B 805 "
            pdb=" CB  ILE B 805 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.78   -0.35 2.00e-01 2.50e+01 3.01e+00
  ... (remaining 2449 not shown)

  Planarity restraints: 2594
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 894 "    0.021 2.00e-02 2.50e+03   4.39e-02 1.92e+01
        pdb=" C   LYS B 894 "   -0.076 2.00e-02 2.50e+03
        pdb=" O   LYS B 894 "    0.029 2.00e-02 2.50e+03
        pdb=" N   THR B 895 "    0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 894 "    0.021 2.00e-02 2.50e+03   4.38e-02 1.92e+01
        pdb=" C   LYS A 894 "   -0.076 2.00e-02 2.50e+03
        pdb=" O   LYS A 894 "    0.029 2.00e-02 2.50e+03
        pdb=" N   THR A 895 "    0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 733 "    0.021 2.00e-02 2.50e+03   4.30e-02 1.85e+01
        pdb=" C   LEU A 733 "   -0.074 2.00e-02 2.50e+03
        pdb=" O   LEU A 733 "    0.027 2.00e-02 2.50e+03
        pdb=" N   LEU A 734 "    0.026 2.00e-02 2.50e+03
  ... (remaining 2591 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1766
        2.75 -     3.28: 15084
        3.28 -     3.82: 23909
        3.82 -     4.36: 29248
        4.36 -     4.90: 51687
  Nonbonded interactions: 121694
  Sorted by model distance:
  nonbonded pdb=" O   LYS B 699 "
            pdb=" OD1 ASN B 703 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" O   LYS A 699 "
            pdb=" OD1 ASN A 703 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" OD1 ASP A 696 "
            pdb=" OG1 THR B 480 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" O   SER A 282 "
            pdb=" OG  SER A 282 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" O   SER B 282 "
            pdb=" OG  SER B 282 "
     model   vdw
     2.260 3.040
  ... (remaining 121689 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: 0.08
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.780
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.550
  Check model and map are aligned:         0.110
  Set scattering table:                    0.140
  Process input model:                     45.600
  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:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   50.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
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      :  0.007   0.071  15428  Z= 0.496
  Angle     :  1.110  10.951  20902  Z= 0.813
  Chirality :  0.063   0.374   2452
  Planarity :  0.006   0.049   2594
  Dihedral  : 15.580 126.673   5640
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 15.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 14.15 %
    Favored  : 84.31 %
  Cbeta Deviations :  0.11 %
  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: -1.69 (0.18), residues: 1896
  helix: -0.59 (0.14), residues: 1220
  sheet:  0.54 (0.48), residues: 92
  loop : -2.35 (0.23), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP B 759 
 HIS   0.017   0.001   HIS A 319 
 PHE   0.029   0.002   PHE A 814 
 TYR   0.009   0.001   TYR A 800 
 ARG   0.005   0.000   ARG A 645 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17699 (  962)
  hydrogen bonds       : angle       7.35268 ( 2814)
  covalent geometry    : bond        0.00668 (15428)
  covalent geometry    : angle       1.11021 (20902)

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

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

  3792 Ramachandran restraints generated.
    1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3792 Ramachandran restraints generated.
    1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  317 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 292
  time to evaluate  : 1.668 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 25
  outliers final: 12
  residues processed: 311
  average time/residue: 0.2926
  time to fit residues: 131.0261
Evaluate side-chains
  213 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 201
  time to evaluate  : 1.826 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  471 ASP
Chi-restraints excluded: chain A residue  761 VAL
Chi-restraints excluded: chain B residue    9 ASP
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  235 ILE
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  471 ASP
Chi-restraints excluded: chain B residue  761 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 160 optimal weight:    0.0040
   chunk 144 optimal weight:    0.9980
   chunk 79 optimal weight:    0.8980
   chunk 49 optimal weight:    0.5980
   chunk 97 optimal weight:    3.9990
   chunk 76 optimal weight:    1.9990
   chunk 148 optimal weight:    0.9980
   chunk 57 optimal weight:    3.9990
   chunk 90 optimal weight:    1.9990
   chunk 110 optimal weight:    2.9990
   chunk 172 optimal weight:    4.9990
   overall best weight:    0.6992

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

Flipped N/Q/H residues before XYZ refinement:
A 298 ASN
A 394 HIS
A 870 ASN
A 897 ASN
B 298 ASN
B 394 HIS
B 418 ASN
B 673 GLN
B 897 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.102559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.076398 restraints weight = 29573.773|
|-----------------------------------------------------------------------------|
r_work (start): 0.2930 rms_B_bonded: 3.31
r_work: 0.2757 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.2757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.2000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  15428  Z= 0.130
  Angle     :  0.566   7.644  20902  Z= 0.297
  Chirality :  0.039   0.144   2452
  Planarity :  0.004   0.043   2594
  Dihedral  :  8.761 127.076   2158
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 16.79 %
    Favored  : 80.09 %
  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:  0.27 (0.19), residues: 1896
  helix:  0.98 (0.15), residues: 1252
  sheet:  1.17 (0.53), residues: 82
  loop : -1.76 (0.24), residues: 562

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 985 
 HIS   0.006   0.001   HIS A 719 
 PHE   0.011   0.001   PHE B 616 
 TYR   0.015   0.001   TYR B 586 
 ARG   0.007   0.000   ARG A 866 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04271 (  962)
  hydrogen bonds       : angle       4.43315 ( 2814)
  covalent geometry    : bond        0.00290 (15428)
  covalent geometry    : angle       0.56580 (20902)

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

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

  3792 Ramachandran restraints generated.
    1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3792 Ramachandran restraints generated.
    1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  288 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 237
  time to evaluate  : 2.020 
Fit side-chains
REVERT: A   30 ARG cc_start: 0.8900 (ttm-80) cc_final: 0.8448 (tpp80)
REVERT: A  147 ASP cc_start: 0.8317 (t0) cc_final: 0.8094 (t0)
REVERT: A  163 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8348 (ptmt)
REVERT: A  323 HIS cc_start: 0.8313 (OUTLIER) cc_final: 0.7314 (m-70)
REVERT: A  685 GLU cc_start: 0.8453 (mp0) cc_final: 0.7813 (mp0)
REVERT: A  706 LEU cc_start: 0.8650 (pt) cc_final: 0.8037 (mt)
REVERT: A  711 ARG cc_start: 0.9190 (OUTLIER) cc_final: 0.8646 (mpp80)
REVERT: A  776 ARG cc_start: 0.9092 (tpp-160) cc_final: 0.8762 (mmm160)
REVERT: A  847 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8259 (tt)
REVERT: A  849 MET cc_start: 0.9192 (OUTLIER) cc_final: 0.8938 (tpp)
REVERT: B   95 HIS cc_start: 0.8278 (p90) cc_final: 0.7238 (p90)
REVERT: B   96 GLN cc_start: 0.9016 (mt0) cc_final: 0.8749 (mp10)
REVERT: B  147 ASP cc_start: 0.8345 (t0) cc_final: 0.8075 (t0)
REVERT: B  163 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8358 (ptmt)
REVERT: B  224 LEU cc_start: 0.9064 (mt) cc_final: 0.8830 (tt)
REVERT: B  284 GLN cc_start: 0.8297 (tp40) cc_final: 0.8085 (tp-100)
REVERT: B  323 HIS cc_start: 0.8360 (OUTLIER) cc_final: 0.7314 (m-70)
REVERT: B  706 LEU cc_start: 0.8600 (pt) cc_final: 0.8025 (mt)
REVERT: B  711 ARG cc_start: 0.9233 (OUTLIER) cc_final: 0.8743 (mpp80)
REVERT: B  776 ARG cc_start: 0.9106 (tpp-160) cc_final: 0.8779 (mmm160)
REVERT: B  847 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8219 (tt)
REVERT: B  849 MET cc_start: 0.9252 (tpp) cc_final: 0.8864 (tpp)
  outliers start: 51
  outliers final: 21
  residues processed: 268
  average time/residue: 0.2630
  time to fit residues: 105.6115
Evaluate side-chains
  240 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 210
  time to evaluate  : 1.677 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  163 LYS
Chi-restraints excluded: chain A residue  169 GLU
Chi-restraints excluded: chain A residue  282 SER
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  323 HIS
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  707 VAL
Chi-restraints excluded: chain A residue  711 ARG
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain A residue  810 VAL
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue  847 LEU
Chi-restraints excluded: chain A residue  849 MET
Chi-restraints excluded: chain A residue  863 ILE
Chi-restraints excluded: chain A residue  864 THR
Chi-restraints excluded: chain A residue  885 ILE
Chi-restraints excluded: chain A residue  902 THR
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain B residue  163 LYS
Chi-restraints excluded: chain B residue  282 SER
Chi-restraints excluded: chain B residue  301 ILE
Chi-restraints excluded: chain B residue  323 HIS
Chi-restraints excluded: chain B residue  368 VAL
Chi-restraints excluded: chain B residue  707 VAL
Chi-restraints excluded: chain B residue  711 ARG
Chi-restraints excluded: chain B residue  810 VAL
Chi-restraints excluded: chain B residue  847 LEU
Chi-restraints excluded: chain B residue  863 ILE
Chi-restraints excluded: chain B residue  885 ILE
Chi-restraints excluded: chain B residue  919 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 41 optimal weight:    6.9990
   chunk 87 optimal weight:    0.6980
   chunk 40 optimal weight:    4.9990
   chunk 159 optimal weight:    4.9990
   chunk 165 optimal weight:    4.9990
   chunk 61 optimal weight:    2.9990
   chunk 128 optimal weight:    0.9980
   chunk 39 optimal weight:    0.4980
   chunk 126 optimal weight:   20.0000
   chunk 143 optimal weight:    3.9990
   chunk 31 optimal weight:    7.9990
   overall best weight:    1.8384

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

Flipped N/Q/H residues before XYZ refinement:
** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 298 ASN
** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 284 GLN
B 298 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.098185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.071145 restraints weight = 30345.995|
|-----------------------------------------------------------------------------|
r_work (start): 0.2884 rms_B_bonded: 3.42
r_work: 0.2714 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.2714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.2489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  15428  Z= 0.170
  Angle     :  0.557   6.530  20902  Z= 0.292
  Chirality :  0.040   0.206   2452
  Planarity :  0.004   0.039   2594
  Dihedral  :  8.271 110.699   2140
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 17.40 %
    Favored  : 78.98 %
  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:  1.16 (0.20), residues: 1896
  helix:  1.69 (0.15), residues: 1248
  sheet:  1.38 (0.53), residues: 82
  loop : -1.46 (0.24), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 985 
 HIS   0.005   0.001   HIS B 606 
 PHE   0.024   0.001   PHE B 195 
 TYR   0.010   0.001   TYR B 129 
 ARG   0.005   0.000   ARG B 866 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04480 (  962)
  hydrogen bonds       : angle       4.16528 ( 2814)
  covalent geometry    : bond        0.00395 (15428)
  covalent geometry    : angle       0.55700 (20902)

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

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

  3792 Ramachandran restraints generated.
    1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3792 Ramachandran restraints generated.
    1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 209
  time to evaluate  : 1.857 
Fit side-chains
REVERT: A  147 ASP cc_start: 0.8413 (t0) cc_final: 0.8168 (t0)
REVERT: A  284 GLN cc_start: 0.8440 (tp-100) cc_final: 0.7924 (tp-100)
REVERT: A  323 HIS cc_start: 0.8408 (OUTLIER) cc_final: 0.7444 (m-70)
REVERT: A  685 GLU cc_start: 0.8636 (mp0) cc_final: 0.7981 (mp0)
REVERT: A  706 LEU cc_start: 0.8692 (pt) cc_final: 0.8128 (mt)
REVERT: A  711 ARG cc_start: 0.9185 (OUTLIER) cc_final: 0.8647 (mpp80)
REVERT: A  776 ARG cc_start: 0.9124 (tpp-160) cc_final: 0.8790 (mmm160)
REVERT: A  849 MET cc_start: 0.9162 (OUTLIER) cc_final: 0.8943 (tpp)
REVERT: B   95 HIS cc_start: 0.8419 (p90) cc_final: 0.8190 (p90)
REVERT: B  147 ASP cc_start: 0.8434 (t0) cc_final: 0.8164 (t0)
REVERT: B  284 GLN cc_start: 0.8546 (tp-100) cc_final: 0.8080 (tp-100)
REVERT: B  323 HIS cc_start: 0.8420 (OUTLIER) cc_final: 0.7443 (m-70)
REVERT: B  541 ARG cc_start: 0.8643 (mtp180) cc_final: 0.8236 (mtp180)
REVERT: B  685 GLU cc_start: 0.8616 (mp0) cc_final: 0.8040 (mp0)
REVERT: B  706 LEU cc_start: 0.8711 (pt) cc_final: 0.8142 (mt)
REVERT: B  776 ARG cc_start: 0.9135 (tpp-160) cc_final: 0.8807 (mmm160)
REVERT: B  847 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8496 (tt)
REVERT: B  849 MET cc_start: 0.9254 (tpp) cc_final: 0.8887 (tpp)
  outliers start: 59
  outliers final: 34
  residues processed: 246
  average time/residue: 0.2621
  time to fit residues: 98.3332
Evaluate side-chains
  231 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 192
  time to evaluate  : 1.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  281 ASP
Chi-restraints excluded: chain A residue  282 SER
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  323 HIS
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  711 ARG
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain A residue  810 VAL
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue  846 LEU
Chi-restraints excluded: chain A residue  849 MET
Chi-restraints excluded: chain A residue  863 ILE
Chi-restraints excluded: chain A residue  864 THR
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  885 ILE
Chi-restraints excluded: chain A residue  902 THR
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  930 CYS
Chi-restraints excluded: chain B residue    9 ASP
Chi-restraints excluded: chain B residue   34 VAL
Chi-restraints excluded: chain B residue   93 GLU
Chi-restraints excluded: chain B residue  281 ASP
Chi-restraints excluded: chain B residue  282 SER
Chi-restraints excluded: chain B residue  301 ILE
Chi-restraints excluded: chain B residue  323 HIS
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  368 VAL
Chi-restraints excluded: chain B residue  680 LEU
Chi-restraints excluded: chain B residue  810 VAL
Chi-restraints excluded: chain B residue  847 LEU
Chi-restraints excluded: chain B residue  863 ILE
Chi-restraints excluded: chain B residue  868 THR
Chi-restraints excluded: chain B residue  871 ILE
Chi-restraints excluded: chain B residue  885 ILE
Chi-restraints excluded: chain B residue  919 LEU
Chi-restraints excluded: chain B residue  930 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 85 optimal weight:    0.1980
   chunk 143 optimal weight:    3.9990
   chunk 9 optimal weight:    6.9990
   chunk 23 optimal weight:    1.9990
   chunk 67 optimal weight:    6.9990
   chunk 13 optimal weight:    4.9990
   chunk 94 optimal weight:    0.9990
   chunk 129 optimal weight:    3.9990
   chunk 146 optimal weight:    4.9990
   chunk 125 optimal weight:    0.9980
   overall best weight:    1.4386

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

Flipped N/Q/H residues before XYZ refinement:
A 103 GLN
** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 298 ASN
** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 103 GLN
B 298 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.098763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.071819 restraints weight = 30105.105|
|-----------------------------------------------------------------------------|
r_work (start): 0.2898 rms_B_bonded: 3.41
r_work: 0.2727 rms_B_bonded: 4.22 restraints_weight: 0.5000
r_work (final): 0.2727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.2783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  15428  Z= 0.144
  Angle     :  0.535   7.968  20902  Z= 0.278
  Chirality :  0.039   0.144   2452
  Planarity :  0.004   0.042   2594
  Dihedral  :  7.853  87.928   2140
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 18.75 %
    Favored  : 78.55 %
  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:  1.64 (0.20), residues: 1896
  helix:  2.09 (0.15), residues: 1236
  sheet:  1.66 (0.57), residues: 72
  loop : -1.24 (0.24), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 985 
 HIS   0.005   0.001   HIS B 606 
 PHE   0.009   0.001   PHE A 117 
 TYR   0.009   0.001   TYR A 245 
 ARG   0.004   0.000   ARG B 433 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04152 (  962)
  hydrogen bonds       : angle       4.02810 ( 2814)
  covalent geometry    : bond        0.00332 (15428)
  covalent geometry    : angle       0.53498 (20902)

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

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

  3792 Ramachandran restraints generated.
    1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3792 Ramachandran restraints generated.
    1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 206
  time to evaluate  : 1.837 
Fit side-chains
REVERT: A  174 MET cc_start: 0.9010 (mmm) cc_final: 0.8762 (mpp)
REVERT: A  284 GLN cc_start: 0.8454 (tp-100) cc_final: 0.7932 (tp-100)
REVERT: A  323 HIS cc_start: 0.8303 (OUTLIER) cc_final: 0.7397 (m-70)
REVERT: A  541 ARG cc_start: 0.8977 (ttp-170) cc_final: 0.8763 (ttp-170)
REVERT: A  685 GLU cc_start: 0.8654 (mp0) cc_final: 0.8065 (mp0)
REVERT: A  706 LEU cc_start: 0.8752 (pt) cc_final: 0.8199 (mt)
REVERT: A  711 ARG cc_start: 0.9187 (OUTLIER) cc_final: 0.8656 (mpp80)
REVERT: A  776 ARG cc_start: 0.9052 (tpp-160) cc_final: 0.8779 (mmm160)
REVERT: A  847 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8348 (tt)
REVERT: B  147 ASP cc_start: 0.8361 (t0) cc_final: 0.8160 (t0)
REVERT: B  174 MET cc_start: 0.9007 (mmm) cc_final: 0.8758 (mpp)
REVERT: B  284 GLN cc_start: 0.8559 (tp-100) cc_final: 0.8131 (tp-100)
REVERT: B  323 HIS cc_start: 0.8377 (OUTLIER) cc_final: 0.7421 (m-70)
REVERT: B  685 GLU cc_start: 0.8682 (mp0) cc_final: 0.8127 (mp0)
REVERT: B  686 MET cc_start: 0.8685 (tpp) cc_final: 0.8443 (tpt)
REVERT: B  706 LEU cc_start: 0.8739 (pt) cc_final: 0.8200 (mt)
REVERT: B  711 ARG cc_start: 0.9221 (OUTLIER) cc_final: 0.8682 (mpp80)
REVERT: B  776 ARG cc_start: 0.9063 (tpp-160) cc_final: 0.8789 (mmm160)
REVERT: B  847 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8411 (tt)
REVERT: B  849 MET cc_start: 0.9247 (tpp) cc_final: 0.8901 (tpp)
  outliers start: 44
  outliers final: 26
  residues processed: 236
  average time/residue: 0.2453
  time to fit residues: 88.9527
Evaluate side-chains
  226 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 194
  time to evaluate  : 1.642 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   93 GLU
Chi-restraints excluded: chain A residue  281 ASP
Chi-restraints excluded: chain A residue  282 SER
Chi-restraints excluded: chain A residue  298 ASN
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  323 HIS
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  711 ARG
Chi-restraints excluded: chain A residue  810 VAL
Chi-restraints excluded: chain A residue  847 LEU
Chi-restraints excluded: chain A residue  863 ILE
Chi-restraints excluded: chain A residue  864 THR
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  885 ILE
Chi-restraints excluded: chain A residue  902 THR
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  930 CYS
Chi-restraints excluded: chain B residue    9 ASP
Chi-restraints excluded: chain B residue   93 GLU
Chi-restraints excluded: chain B residue  298 ASN
Chi-restraints excluded: chain B residue  301 ILE
Chi-restraints excluded: chain B residue  323 HIS
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  711 ARG
Chi-restraints excluded: chain B residue  810 VAL
Chi-restraints excluded: chain B residue  847 LEU
Chi-restraints excluded: chain B residue  863 ILE
Chi-restraints excluded: chain B residue  868 THR
Chi-restraints excluded: chain B residue  885 ILE
Chi-restraints excluded: chain B residue  930 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 134 optimal weight:    0.8980
   chunk 32 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   chunk 11 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9990
   chunk 175 optimal weight:    0.0970
   chunk 50 optimal weight:    4.9990
   chunk 154 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 124 optimal weight:    1.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 298 ASN
A 674 ASN
** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 298 ASN
B 674 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.100249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.073570 restraints weight = 30081.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.2930 rms_B_bonded: 3.37
r_work: 0.2762 rms_B_bonded: 4.21 restraints_weight: 0.5000
r_work (final): 0.2762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.3060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  15428  Z= 0.114
  Angle     :  0.518  10.480  20902  Z= 0.266
  Chirality :  0.038   0.134   2452
  Planarity :  0.004   0.041   2594
  Dihedral  :  7.498  81.251   2140
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 19.12 %
    Favored  : 78.62 %
  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:  1.92 (0.20), residues: 1896
  helix:  2.33 (0.15), residues: 1236
  sheet:  1.75 (0.58), residues: 72
  loop : -1.19 (0.24), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 985 
 HIS   0.004   0.001   HIS A 606 
 PHE   0.010   0.001   PHE B 117 
 TYR   0.009   0.001   TYR B 245 
 ARG   0.004   0.000   ARG A 433 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03785 (  962)
  hydrogen bonds       : angle       3.91661 ( 2814)
  covalent geometry    : bond        0.00253 (15428)
  covalent geometry    : angle       0.51823 (20902)

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

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

  3792 Ramachandran restraints generated.
    1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3792 Ramachandran restraints generated.
    1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 208
  time to evaluate  : 2.507 
Fit side-chains
REVERT: A  284 GLN cc_start: 0.8431 (tp-100) cc_final: 0.7895 (tp-100)
REVERT: A  323 HIS cc_start: 0.8223 (OUTLIER) cc_final: 0.7399 (m-70)
REVERT: A  541 ARG cc_start: 0.8986 (ttp-170) cc_final: 0.8739 (ttp-110)
REVERT: A  685 GLU cc_start: 0.8783 (mp0) cc_final: 0.8234 (mp0)
REVERT: A  706 LEU cc_start: 0.8714 (pt) cc_final: 0.8313 (mt)
REVERT: A  709 MET cc_start: 0.8510 (mmm) cc_final: 0.8207 (mmm)
REVERT: A  711 ARG cc_start: 0.9170 (OUTLIER) cc_final: 0.8633 (mpp80)
REVERT: A  776 ARG cc_start: 0.8977 (tpp-160) cc_final: 0.8666 (mmm160)
REVERT: A  847 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8394 (tt)
REVERT: B  284 GLN cc_start: 0.8510 (tp-100) cc_final: 0.8113 (tp-100)
REVERT: B  323 HIS cc_start: 0.8278 (OUTLIER) cc_final: 0.7433 (m-70)
REVERT: B  685 GLU cc_start: 0.8771 (mp0) cc_final: 0.8168 (mp0)
REVERT: B  706 LEU cc_start: 0.8768 (pt) cc_final: 0.8329 (mt)
REVERT: B  711 ARG cc_start: 0.9217 (OUTLIER) cc_final: 0.8687 (mpp80)
REVERT: B  776 ARG cc_start: 0.9016 (tpp-160) cc_final: 0.8753 (mmm160)
REVERT: B  849 MET cc_start: 0.9197 (tpp) cc_final: 0.8840 (tpp)
REVERT: B 1024 MET cc_start: 0.8885 (mtp) cc_final: 0.8611 (mmm)
  outliers start: 37
  outliers final: 22
  residues processed: 236
  average time/residue: 0.3672
  time to fit residues: 132.0391
Evaluate side-chains
  219 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 192
  time to evaluate  : 2.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue  282 SER
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  323 HIS
Chi-restraints excluded: chain A residue  711 ARG
Chi-restraints excluded: chain A residue  810 VAL
Chi-restraints excluded: chain A residue  847 LEU
Chi-restraints excluded: chain A residue  863 ILE
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  871 ILE
Chi-restraints excluded: chain A residue  885 ILE
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  930 CYS
Chi-restraints excluded: chain B residue    9 ASP
Chi-restraints excluded: chain B residue   34 VAL
Chi-restraints excluded: chain B residue   93 GLU
Chi-restraints excluded: chain B residue  281 ASP
Chi-restraints excluded: chain B residue  301 ILE
Chi-restraints excluded: chain B residue  323 HIS
Chi-restraints excluded: chain B residue  460 LEU
Chi-restraints excluded: chain B residue  680 LEU
Chi-restraints excluded: chain B residue  711 ARG
Chi-restraints excluded: chain B residue  810 VAL
Chi-restraints excluded: chain B residue  863 ILE
Chi-restraints excluded: chain B residue  868 THR
Chi-restraints excluded: chain B residue  885 ILE
Chi-restraints excluded: chain B residue  930 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 97 optimal weight:    3.9990
   chunk 71 optimal weight:    5.9990
   chunk 73 optimal weight:    0.7980
   chunk 120 optimal weight:    1.9990
   chunk 54 optimal weight:    0.8980
   chunk 19 optimal weight:    8.9990
   chunk 40 optimal weight:    3.9990
   chunk 145 optimal weight:    0.8980
   chunk 130 optimal weight:    6.9990
   chunk 29 optimal weight:    0.7980
   chunk 10 optimal weight:    0.0470
   overall best weight:    0.6878

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

Flipped N/Q/H residues before XYZ refinement:
** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 673 GLN
** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.101570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.074458 restraints weight = 30100.350|
|-----------------------------------------------------------------------------|
r_work (start): 0.2952 rms_B_bonded: 3.41
r_work: 0.2783 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.2783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.3313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  15428  Z= 0.109
  Angle     :  0.515  10.702  20902  Z= 0.264
  Chirality :  0.038   0.163   2452
  Planarity :  0.003   0.040   2594
  Dihedral  :  6.706  84.207   2140
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 20.34 %
    Favored  : 77.82 %
  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:  2.05 (0.20), residues: 1896
  helix:  2.47 (0.15), residues: 1232
  sheet:  1.87 (0.57), residues: 72
  loop : -1.23 (0.23), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 985 
 HIS   0.004   0.001   HIS A 606 
 PHE   0.027   0.001   PHE A 195 
 TYR   0.009   0.001   TYR A 245 
 ARG   0.007   0.000   ARG A 866 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03569 (  962)
  hydrogen bonds       : angle       3.81945 ( 2814)
  covalent geometry    : bond        0.00243 (15428)
  covalent geometry    : angle       0.51518 (20902)

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

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

  3792 Ramachandran restraints generated.
    1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3792 Ramachandran restraints generated.
    1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 221
  time to evaluate  : 1.827 
Fit side-chains
REVERT: A  232 ASP cc_start: 0.8770 (OUTLIER) cc_final: 0.8535 (t0)
REVERT: A  284 GLN cc_start: 0.8425 (tp-100) cc_final: 0.7881 (tp-100)
REVERT: A  323 HIS cc_start: 0.8230 (OUTLIER) cc_final: 0.7382 (m-70)
REVERT: A  541 ARG cc_start: 0.8996 (ttp-170) cc_final: 0.8745 (ttp-110)
REVERT: A  685 GLU cc_start: 0.8832 (mp0) cc_final: 0.8396 (mp0)
REVERT: A  706 LEU cc_start: 0.8748 (pt) cc_final: 0.8344 (mt)
REVERT: A  711 ARG cc_start: 0.9177 (OUTLIER) cc_final: 0.8599 (mpp80)
REVERT: A  776 ARG cc_start: 0.8941 (tpp-160) cc_final: 0.8679 (mmm160)
REVERT: A  847 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8357 (tt)
REVERT: A  866 ARG cc_start: 0.8951 (ttm110) cc_final: 0.8668 (mtt-85)
REVERT: B   74 ASP cc_start: 0.8876 (m-30) cc_final: 0.8650 (p0)
REVERT: B  284 GLN cc_start: 0.8486 (tp-100) cc_final: 0.8025 (tp-100)
REVERT: B  323 HIS cc_start: 0.8251 (OUTLIER) cc_final: 0.7404 (m-70)
REVERT: B  682 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7469 (mt-10)
REVERT: B  685 GLU cc_start: 0.8801 (mp0) cc_final: 0.8299 (mp0)
REVERT: B  706 LEU cc_start: 0.8781 (pt) cc_final: 0.8384 (mt)
REVERT: B  709 MET cc_start: 0.8474 (mmm) cc_final: 0.8224 (mmm)
REVERT: B  711 ARG cc_start: 0.9189 (OUTLIER) cc_final: 0.8673 (mpp80)
REVERT: B  776 ARG cc_start: 0.8986 (tpp-160) cc_final: 0.8528 (mmm-85)
REVERT: B  847 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8546 (tt)
REVERT: B  849 MET cc_start: 0.9205 (tpp) cc_final: 0.8929 (tpp)
  outliers start: 30
  outliers final: 21
  residues processed: 240
  average time/residue: 0.2652
  time to fit residues: 97.8510
Evaluate side-chains
  236 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 208
  time to evaluate  : 1.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  232 ASP
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  323 HIS
Chi-restraints excluded: chain A residue  711 ARG
Chi-restraints excluded: chain A residue  810 VAL
Chi-restraints excluded: chain A residue  847 LEU
Chi-restraints excluded: chain A residue  863 ILE
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  871 ILE
Chi-restraints excluded: chain A residue  885 ILE
Chi-restraints excluded: chain A residue  930 CYS
Chi-restraints excluded: chain B residue    9 ASP
Chi-restraints excluded: chain B residue   34 VAL
Chi-restraints excluded: chain B residue   93 GLU
Chi-restraints excluded: chain B residue  281 ASP
Chi-restraints excluded: chain B residue  301 ILE
Chi-restraints excluded: chain B residue  323 HIS
Chi-restraints excluded: chain B residue  460 LEU
Chi-restraints excluded: chain B residue  711 ARG
Chi-restraints excluded: chain B residue  810 VAL
Chi-restraints excluded: chain B residue  847 LEU
Chi-restraints excluded: chain B residue  863 ILE
Chi-restraints excluded: chain B residue  867 SER
Chi-restraints excluded: chain B residue  868 THR
Chi-restraints excluded: chain B residue  885 ILE
Chi-restraints excluded: chain B residue  930 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 85 optimal weight:    0.0270
   chunk 27 optimal weight:    0.8980
   chunk 81 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   chunk 53 optimal weight:    4.9990
   chunk 162 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 60 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0060
   chunk 100 optimal weight:    3.9990
   overall best weight:    0.5454

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

Flipped N/Q/H residues before XYZ refinement:
A  70 ASN
** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 674 ASN
** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  70 ASN
** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 674 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.102390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.075377 restraints weight = 30592.738|
|-----------------------------------------------------------------------------|
r_work (start): 0.2971 rms_B_bonded: 3.44
r_work: 0.2803 rms_B_bonded: 4.27 restraints_weight: 0.5000
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.3517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  15428  Z= 0.106
  Angle     :  0.520  11.282  20902  Z= 0.267
  Chirality :  0.038   0.165   2452
  Planarity :  0.003   0.038   2594
  Dihedral  :  6.473  86.147   2140
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 20.71 %
    Favored  : 77.39 %
  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:  2.16 (0.20), residues: 1896
  helix:  2.57 (0.15), residues: 1236
  sheet:  1.69 (0.54), residues: 82
  loop : -1.28 (0.24), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 985 
 HIS   0.005   0.001   HIS B 319 
 PHE   0.012   0.001   PHE A 228 
 TYR   0.009   0.001   TYR A 245 
 ARG   0.005   0.000   ARG A 866 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03441 (  962)
  hydrogen bonds       : angle       3.76936 ( 2814)
  covalent geometry    : bond        0.00235 (15428)
  covalent geometry    : angle       0.51996 (20902)

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

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

  3792 Ramachandran restraints generated.
    1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3792 Ramachandran restraints generated.
    1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 222
  time to evaluate  : 1.671 
Fit side-chains
REVERT: A  117 PHE cc_start: 0.8992 (m-80) cc_final: 0.8671 (m-10)
REVERT: A  171 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8303 (tm-30)
REVERT: A  284 GLN cc_start: 0.8424 (tp-100) cc_final: 0.7873 (tp-100)
REVERT: A  292 MET cc_start: 0.8952 (tpp) cc_final: 0.8703 (tpp)
REVERT: A  323 HIS cc_start: 0.8133 (OUTLIER) cc_final: 0.7380 (m-70)
REVERT: A  541 ARG cc_start: 0.8983 (ttp-170) cc_final: 0.8717 (ttp-110)
REVERT: A  685 GLU cc_start: 0.8921 (mp0) cc_final: 0.8392 (mp0)
REVERT: A  706 LEU cc_start: 0.8795 (pt) cc_final: 0.8435 (mt)
REVERT: A  711 ARG cc_start: 0.9159 (OUTLIER) cc_final: 0.8633 (mpp80)
REVERT: A  776 ARG cc_start: 0.8927 (tpp-160) cc_final: 0.8490 (mmm160)
REVERT: A  847 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8292 (tt)
REVERT: B   74 ASP cc_start: 0.8867 (m-30) cc_final: 0.8650 (p0)
REVERT: B  117 PHE cc_start: 0.8979 (m-80) cc_final: 0.8672 (m-10)
REVERT: B  171 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8280 (tm-30)
REVERT: B  284 GLN cc_start: 0.8487 (tp-100) cc_final: 0.8034 (tp-100)
REVERT: B  323 HIS cc_start: 0.8195 (OUTLIER) cc_final: 0.7401 (m-70)
REVERT: B  545 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8664 (pt0)
REVERT: B  685 GLU cc_start: 0.8833 (mp0) cc_final: 0.8418 (mp0)
REVERT: B  706 LEU cc_start: 0.8700 (pt) cc_final: 0.8311 (mt)
REVERT: B  711 ARG cc_start: 0.9194 (OUTLIER) cc_final: 0.8685 (mpp80)
REVERT: B  776 ARG cc_start: 0.8943 (tpp-160) cc_final: 0.8485 (mmm-85)
REVERT: B  847 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8497 (tt)
REVERT: B  849 MET cc_start: 0.9189 (tpp) cc_final: 0.8934 (tpp)
  outliers start: 31
  outliers final: 20
  residues processed: 241
  average time/residue: 0.2450
  time to fit residues: 89.9255
Evaluate side-chains
  241 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 214
  time to evaluate  : 1.730 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  323 HIS
Chi-restraints excluded: chain A residue  711 ARG
Chi-restraints excluded: chain A residue  810 VAL
Chi-restraints excluded: chain A residue  847 LEU
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  871 ILE
Chi-restraints excluded: chain A residue  885 ILE
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  930 CYS
Chi-restraints excluded: chain B residue    9 ASP
Chi-restraints excluded: chain B residue   34 VAL
Chi-restraints excluded: chain B residue   93 GLU
Chi-restraints excluded: chain B residue  281 ASP
Chi-restraints excluded: chain B residue  301 ILE
Chi-restraints excluded: chain B residue  323 HIS
Chi-restraints excluded: chain B residue  460 LEU
Chi-restraints excluded: chain B residue  545 GLU
Chi-restraints excluded: chain B residue  711 ARG
Chi-restraints excluded: chain B residue  810 VAL
Chi-restraints excluded: chain B residue  847 LEU
Chi-restraints excluded: chain B residue  867 SER
Chi-restraints excluded: chain B residue  868 THR
Chi-restraints excluded: chain B residue  885 ILE
Chi-restraints excluded: chain B residue  930 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 161 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 143 optimal weight:    6.9990
   chunk 182 optimal weight:    3.9990
   chunk 109 optimal weight:    0.3980
   chunk 162 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   chunk 144 optimal weight:    0.7980
   chunk 158 optimal weight:    0.9990
   chunk 139 optimal weight:    3.9990
   chunk 103 optimal weight:    1.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 674 ASN
** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 674 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.101834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.074803 restraints weight = 30214.633|
|-----------------------------------------------------------------------------|
r_work (start): 0.2961 rms_B_bonded: 3.40
r_work: 0.2791 rms_B_bonded: 4.27 restraints_weight: 0.5000
r_work (final): 0.2791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.3611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  15428  Z= 0.114
  Angle     :  0.524  11.010  20902  Z= 0.268
  Chirality :  0.038   0.165   2452
  Planarity :  0.004   0.045   2594
  Dihedral  :  6.371  83.081   2140
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 20.71 %
    Favored  : 77.27 %
  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:  2.23 (0.20), residues: 1896
  helix:  2.64 (0.15), residues: 1232
  sheet:  1.97 (0.56), residues: 72
  loop : -1.24 (0.23), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 985 
 HIS   0.006   0.001   HIS B 319 
 PHE   0.012   0.001   PHE B 228 
 TYR   0.011   0.001   TYR A 129 
 ARG   0.012   0.000   ARG B 866 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03562 (  962)
  hydrogen bonds       : angle       3.76977 ( 2814)
  covalent geometry    : bond        0.00262 (15428)
  covalent geometry    : angle       0.52355 (20902)

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

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

  3792 Ramachandran restraints generated.
    1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3792 Ramachandran restraints generated.
    1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 217
  time to evaluate  : 2.124 
Fit side-chains
REVERT: A  117 PHE cc_start: 0.8988 (m-80) cc_final: 0.8640 (m-10)
REVERT: A  171 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8296 (tm-30)
REVERT: A  284 GLN cc_start: 0.8450 (tp-100) cc_final: 0.7891 (tp-100)
REVERT: A  323 HIS cc_start: 0.8144 (OUTLIER) cc_final: 0.7412 (m-70)
REVERT: A  541 ARG cc_start: 0.8974 (ttp-170) cc_final: 0.8685 (ttp-110)
REVERT: A  685 GLU cc_start: 0.8883 (mp0) cc_final: 0.8452 (mp0)
REVERT: A  706 LEU cc_start: 0.8832 (pt) cc_final: 0.8466 (mt)
REVERT: A  711 ARG cc_start: 0.9164 (OUTLIER) cc_final: 0.8635 (mpp80)
REVERT: A  776 ARG cc_start: 0.8948 (tpp-160) cc_final: 0.8520 (mmm160)
REVERT: A  847 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8230 (tt)
REVERT: B   74 ASP cc_start: 0.8878 (m-30) cc_final: 0.8647 (p0)
REVERT: B   95 HIS cc_start: 0.8402 (p90) cc_final: 0.8142 (p90)
REVERT: B  117 PHE cc_start: 0.8955 (m-80) cc_final: 0.8619 (m-10)
REVERT: B  171 GLU cc_start: 0.8711 (tm-30) cc_final: 0.8287 (tm-30)
REVERT: B  284 GLN cc_start: 0.8555 (tp-100) cc_final: 0.8069 (tp-100)
REVERT: B  323 HIS cc_start: 0.8218 (OUTLIER) cc_final: 0.7442 (m-70)
REVERT: B  545 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8673 (pt0)
REVERT: B  685 GLU cc_start: 0.8955 (mp0) cc_final: 0.8475 (mp0)
REVERT: B  706 LEU cc_start: 0.8726 (pt) cc_final: 0.8372 (mt)
REVERT: B  711 ARG cc_start: 0.9176 (OUTLIER) cc_final: 0.8698 (mpp80)
REVERT: B  776 ARG cc_start: 0.8952 (tpp-160) cc_final: 0.8522 (mmm-85)
REVERT: B  804 MET cc_start: 0.8999 (mmt) cc_final: 0.8640 (mmt)
REVERT: B  847 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8558 (tt)
REVERT: B  849 MET cc_start: 0.9228 (tpp) cc_final: 0.8958 (tpp)
  outliers start: 33
  outliers final: 25
  residues processed: 237
  average time/residue: 0.2652
  time to fit residues: 94.6826
Evaluate side-chains
  238 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 206
  time to evaluate  : 1.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   93 GLU
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  323 HIS
Chi-restraints excluded: chain A residue  460 LEU
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain A residue  703 ASN
Chi-restraints excluded: chain A residue  711 ARG
Chi-restraints excluded: chain A residue  810 VAL
Chi-restraints excluded: chain A residue  847 LEU
Chi-restraints excluded: chain A residue  863 ILE
Chi-restraints excluded: chain A residue  871 ILE
Chi-restraints excluded: chain A residue  885 ILE
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  930 CYS
Chi-restraints excluded: chain B residue    9 ASP
Chi-restraints excluded: chain B residue   34 VAL
Chi-restraints excluded: chain B residue   93 GLU
Chi-restraints excluded: chain B residue  281 ASP
Chi-restraints excluded: chain B residue  301 ILE
Chi-restraints excluded: chain B residue  323 HIS
Chi-restraints excluded: chain B residue  460 LEU
Chi-restraints excluded: chain B residue  545 GLU
Chi-restraints excluded: chain B residue  711 ARG
Chi-restraints excluded: chain B residue  810 VAL
Chi-restraints excluded: chain B residue  847 LEU
Chi-restraints excluded: chain B residue  863 ILE
Chi-restraints excluded: chain B residue  867 SER
Chi-restraints excluded: chain B residue  868 THR
Chi-restraints excluded: chain B residue  885 ILE
Chi-restraints excluded: chain B residue  930 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 145 optimal weight:    2.9990
   chunk 68 optimal weight:    6.9990
   chunk 70 optimal weight:    0.5980
   chunk 62 optimal weight:    0.7980
   chunk 177 optimal weight:    0.5980
   chunk 97 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9990
   chunk 127 optimal weight:    4.9990
   chunk 160 optimal weight:    2.9990
   chunk 137 optimal weight:    6.9990
   chunk 103 optimal weight:    0.8980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 483 ASN
A 674 ASN
** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.102238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.075265 restraints weight = 30307.331|
|-----------------------------------------------------------------------------|
r_work (start): 0.2967 rms_B_bonded: 3.40
r_work: 0.2799 rms_B_bonded: 4.26 restraints_weight: 0.5000
r_work (final): 0.2799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.3727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  15428  Z= 0.114
  Angle     :  0.533   9.109  20902  Z= 0.270
  Chirality :  0.038   0.171   2452
  Planarity :  0.003   0.039   2594
  Dihedral  :  6.357  84.567   2140
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 21.69 %
    Favored  : 76.41 %
  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:  2.31 (0.20), residues: 1896
  helix:  2.67 (0.15), residues: 1240
  sheet:  2.08 (0.56), residues: 72
  loop : -1.20 (0.23), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 985 
 HIS   0.005   0.001   HIS B 319 
 PHE   0.013   0.001   PHE A 228 
 TYR   0.009   0.001   TYR A 245 
 ARG   0.006   0.000   ARG B 866 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03532 (  962)
  hydrogen bonds       : angle       3.72759 ( 2814)
  covalent geometry    : bond        0.00265 (15428)
  covalent geometry    : angle       0.53295 (20902)

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

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

  3792 Ramachandran restraints generated.
    1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3792 Ramachandran restraints generated.
    1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 212
  time to evaluate  : 1.987 
Fit side-chains
REVERT: A  171 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8303 (tm-30)
REVERT: A  284 GLN cc_start: 0.8432 (tp-100) cc_final: 0.7863 (tp-100)
REVERT: A  323 HIS cc_start: 0.8174 (OUTLIER) cc_final: 0.7456 (m-70)
REVERT: A  541 ARG cc_start: 0.8996 (ttp-170) cc_final: 0.8698 (ttp-110)
REVERT: A  682 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7469 (mt-10)
REVERT: A  685 GLU cc_start: 0.8906 (mp0) cc_final: 0.8446 (mp0)
REVERT: A  706 LEU cc_start: 0.8873 (pt) cc_final: 0.8547 (mt)
REVERT: A  709 MET cc_start: 0.8518 (mmm) cc_final: 0.8205 (mmm)
REVERT: A  711 ARG cc_start: 0.9180 (OUTLIER) cc_final: 0.8655 (mpp80)
REVERT: A  776 ARG cc_start: 0.8956 (tpp-160) cc_final: 0.8525 (mmm160)
REVERT: A  847 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8220 (tt)
REVERT: B   74 ASP cc_start: 0.8878 (m-30) cc_final: 0.8589 (p0)
REVERT: B   95 HIS cc_start: 0.8356 (p90) cc_final: 0.8107 (p90)
REVERT: B  117 PHE cc_start: 0.8966 (m-80) cc_final: 0.8573 (m-10)
REVERT: B  171 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8204 (tm-30)
REVERT: B  284 GLN cc_start: 0.8566 (tp-100) cc_final: 0.8057 (tp-100)
REVERT: B  323 HIS cc_start: 0.8232 (OUTLIER) cc_final: 0.7462 (m-70)
REVERT: B  685 GLU cc_start: 0.8904 (mp0) cc_final: 0.8456 (mp0)
REVERT: B  706 LEU cc_start: 0.8722 (pt) cc_final: 0.8415 (mt)
REVERT: B  776 ARG cc_start: 0.8948 (tpp-160) cc_final: 0.8522 (mmm-85)
REVERT: B  847 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8534 (tt)
REVERT: B  849 MET cc_start: 0.9224 (tpp) cc_final: 0.8963 (tpp)
  outliers start: 31
  outliers final: 23
  residues processed: 230
  average time/residue: 0.3014
  time to fit residues: 106.6429
Evaluate side-chains
  238 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 210
  time to evaluate  : 1.728 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   45 VAL
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  323 HIS
Chi-restraints excluded: chain A residue  460 LEU
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain A residue  711 ARG
Chi-restraints excluded: chain A residue  810 VAL
Chi-restraints excluded: chain A residue  847 LEU
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  871 ILE
Chi-restraints excluded: chain A residue  885 ILE
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  930 CYS
Chi-restraints excluded: chain B residue    9 ASP
Chi-restraints excluded: chain B residue   34 VAL
Chi-restraints excluded: chain B residue   93 GLU
Chi-restraints excluded: chain B residue  281 ASP
Chi-restraints excluded: chain B residue  301 ILE
Chi-restraints excluded: chain B residue  323 HIS
Chi-restraints excluded: chain B residue  460 LEU
Chi-restraints excluded: chain B residue  810 VAL
Chi-restraints excluded: chain B residue  847 LEU
Chi-restraints excluded: chain B residue  867 SER
Chi-restraints excluded: chain B residue  868 THR
Chi-restraints excluded: chain B residue  885 ILE
Chi-restraints excluded: chain B residue  930 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 74 optimal weight:    3.9990
   chunk 153 optimal weight:    3.9990
   chunk 179 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 43 optimal weight:    0.6980
   chunk 115 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   chunk 177 optimal weight:    0.0980
   chunk 86 optimal weight:    8.9990
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 674 ASN
** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 674 ASN
** B 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.104297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.077342 restraints weight = 30268.343|
|-----------------------------------------------------------------------------|
r_work (start): 0.2982 rms_B_bonded: 3.41
r_work: 0.2811 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.2811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.3801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  15428  Z= 0.112
  Angle     :  0.533   9.793  20902  Z= 0.270
  Chirality :  0.038   0.171   2452
  Planarity :  0.004   0.039   2594
  Dihedral  :  6.308  86.026   2140
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 22.24 %
    Favored  : 75.86 %
  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:  2.37 (0.20), residues: 1896
  helix:  2.75 (0.15), residues: 1236
  sheet:  1.87 (0.53), residues: 82
  loop : -1.24 (0.24), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 985 
 HIS   0.004   0.001   HIS B 606 
 PHE   0.011   0.001   PHE A 917 
 TYR   0.009   0.001   TYR A 245 
 ARG   0.008   0.000   ARG B 866 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03479 (  962)
  hydrogen bonds       : angle       3.71777 ( 2814)
  covalent geometry    : bond        0.00258 (15428)
  covalent geometry    : angle       0.53251 (20902)

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

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

  3792 Ramachandran restraints generated.
    1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3792 Ramachandran restraints generated.
    1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 210
  time to evaluate  : 1.993 
Fit side-chains
REVERT: A  171 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8312 (tm-30)
REVERT: A  284 GLN cc_start: 0.8422 (tp-100) cc_final: 0.7847 (tp-100)
REVERT: A  323 HIS cc_start: 0.8271 (OUTLIER) cc_final: 0.7586 (m-70)
REVERT: A  541 ARG cc_start: 0.8992 (ttp-170) cc_final: 0.8693 (ttp-110)
REVERT: A  682 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7476 (mt-10)
REVERT: A  685 GLU cc_start: 0.8867 (mp0) cc_final: 0.8489 (mp0)
REVERT: A  706 LEU cc_start: 0.8836 (pt) cc_final: 0.8541 (mt)
REVERT: A  709 MET cc_start: 0.8531 (mmm) cc_final: 0.8221 (mmm)
REVERT: A  711 ARG cc_start: 0.9183 (OUTLIER) cc_final: 0.8660 (mpp80)
REVERT: A  776 ARG cc_start: 0.8982 (tpp-160) cc_final: 0.8690 (mmm160)
REVERT: A  847 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8382 (tt)
REVERT: B   74 ASP cc_start: 0.8872 (m-30) cc_final: 0.8581 (p0)
REVERT: B   95 HIS cc_start: 0.8354 (p90) cc_final: 0.8083 (p90)
REVERT: B  171 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8277 (tm-30)
REVERT: B  284 GLN cc_start: 0.8550 (tp-100) cc_final: 0.8047 (tp-100)
REVERT: B  323 HIS cc_start: 0.8238 (OUTLIER) cc_final: 0.7487 (m-70)
REVERT: B  460 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8286 (tt)
REVERT: B  685 GLU cc_start: 0.8880 (mp0) cc_final: 0.8506 (mp0)
REVERT: B  706 LEU cc_start: 0.8749 (pt) cc_final: 0.8455 (mt)
REVERT: B  776 ARG cc_start: 0.8923 (tpp-160) cc_final: 0.8330 (mmm160)
REVERT: B  847 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8504 (tt)
REVERT: B  849 MET cc_start: 0.9210 (tpp) cc_final: 0.8952 (tpp)
  outliers start: 31
  outliers final: 24
  residues processed: 228
  average time/residue: 0.2818
  time to fit residues: 98.6804
Evaluate side-chains
  232 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 202
  time to evaluate  : 1.607 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   45 VAL
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  323 HIS
Chi-restraints excluded: chain A residue  460 LEU
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain A residue  711 ARG
Chi-restraints excluded: chain A residue  810 VAL
Chi-restraints excluded: chain A residue  847 LEU
Chi-restraints excluded: chain A residue  863 ILE
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  871 ILE
Chi-restraints excluded: chain A residue  885 ILE
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  930 CYS
Chi-restraints excluded: chain B residue    9 ASP
Chi-restraints excluded: chain B residue   34 VAL
Chi-restraints excluded: chain B residue   93 GLU
Chi-restraints excluded: chain B residue  281 ASP
Chi-restraints excluded: chain B residue  301 ILE
Chi-restraints excluded: chain B residue  323 HIS
Chi-restraints excluded: chain B residue  460 LEU
Chi-restraints excluded: chain B residue  482 LEU
Chi-restraints excluded: chain B residue  810 VAL
Chi-restraints excluded: chain B residue  847 LEU
Chi-restraints excluded: chain B residue  867 SER
Chi-restraints excluded: chain B residue  868 THR
Chi-restraints excluded: chain B residue  885 ILE
Chi-restraints excluded: chain B residue  930 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 67 optimal weight:    0.7980
   chunk 125 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 141 optimal weight:    3.9990
   chunk 126 optimal weight:   10.0000
   chunk 138 optimal weight:    0.7980
   chunk 156 optimal weight:    6.9990
   chunk 1 optimal weight:    2.9990
   chunk 101 optimal weight:    1.9990
   chunk 148 optimal weight:    0.5980
   chunk 164 optimal weight:    0.8980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 674 ASN
** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 674 ASN
** B 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.101824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.074533 restraints weight = 30565.947|
|-----------------------------------------------------------------------------|
r_work (start): 0.2960 rms_B_bonded: 3.44
r_work: 0.2789 rms_B_bonded: 4.30 restraints_weight: 0.5000
r_work (final): 0.2789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.3812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  15428  Z= 0.123
  Angle     :  0.540  10.112  20902  Z= 0.274
  Chirality :  0.039   0.177   2452
  Planarity :  0.004   0.039   2594
  Dihedral  :  6.302  83.332   2140
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 22.24 %
    Favored  : 75.74 %
  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:  2.38 (0.20), residues: 1896
  helix:  2.76 (0.15), residues: 1236
  sheet:  1.75 (0.53), residues: 82
  loop : -1.23 (0.24), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 985 
 HIS   0.006   0.001   HIS B 319 
 PHE   0.020   0.001   PHE B 195 
 TYR   0.010   0.001   TYR A 245 
 ARG   0.008   0.000   ARG B 866 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03646 (  962)
  hydrogen bonds       : angle       3.74269 ( 2814)
  covalent geometry    : bond        0.00290 (15428)
  covalent geometry    : angle       0.53993 (20902)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6911.98 seconds
wall clock time: 125 minutes 46.65 seconds (7546.65 seconds total)