Starting phenix.real_space_refine
on Wed Jun 11 09:01:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bkv_44646/06_2025/9bkv_44646.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bkv_44646/06_2025/9bkv_44646.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.43
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bkv_44646/06_2025/9bkv_44646.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bkv_44646/06_2025/9bkv_44646.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bkv_44646/06_2025/9bkv_44646.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bkv_44646/06_2025/9bkv_44646.cif"
  }
  resolution = 3.43
  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=   0.084
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
     Fe      2      7.16       5
     S      66      5.16       5
     C    7968      2.51       5
     N    2186      2.21       5
     O    2340      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 33 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 12562
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6260
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 788, 6260
          Classifications: {'peptide': 788}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 35, 'TRANS': 752}
    Chain: "B"
      Number of atoms: 6216
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 783, 6216
          Classifications: {'peptide': 783}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 747}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 8.14, per 1000 atoms: 0.65
  Number of scatterers: 12562
  At special positions: 0
  Unit cell: (102.554, 107.882, 198.449, 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)
     Fe      2     26.01
     S      66     16.00
     O    2340      8.00
     N    2186      7.00
     C    7968      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.09
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  3130 Ramachandran restraints generated.
    1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2962

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 16 sheets defined
      47.8% alpha, 22.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.56
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 29
    Processing helix  chain 'A' and resid 46 through 53
    Processing helix  chain 'A' and resid 56 through 61
    Processing helix  chain 'A' and resid 64 through 69
    Processing helix  chain 'A' and resid 70 through 77
      Proline residue:  A  75  - end of helix
    Processing helix  chain 'A' and resid 78 through 88
    Processing helix  chain 'A' and resid 133 through 152
    Processing helix  chain 'A' and resid 170 through 175
    Processing helix  chain 'A' and resid 188 through 193
    Processing helix  chain 'A' and resid 199 through 212
    Processing helix  chain 'A' and resid 257 through 276
      removed outlier: 3.503A  pdb=" N   SER A 275 " --> pdb=" O   ALA A 271 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   SER A 276 " --> pdb=" O   ALA A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 294
    Processing helix  chain 'A' and resid 352 through 382
      removed outlier: 3.583A  pdb=" N   ILE A 356 " --> pdb=" O   THR A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 394 through 408
    Processing helix  chain 'A' and resid 421 through 430
    Processing helix  chain 'A' and resid 430 through 447
      removed outlier: 3.527A  pdb=" N   ALA A 434 " --> pdb=" O   GLY A 430 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   GLN A 436 " --> pdb=" O   ALA A 432 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 471 through 485
      removed outlier: 3.627A  pdb=" N   GLN A 477 " --> pdb=" O   SER A 473 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 530
      removed outlier: 3.841A  pdb=" N   ASN A 530 " --> pdb=" O   TYR A 526 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 539 through 563
      removed outlier: 3.830A  pdb=" N   GLU A 544 " --> pdb=" O   PRO A 540 " (cutoff:3.500A)
      removed outlier: 5.881A  pdb=" N   MET A 545 " --> pdb=" O   ALA A 541 " (cutoff:3.500A)
      removed outlier: 4.400A  pdb=" N   VAL A 546 " --> pdb=" O   MET A 542 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   VAL A 551 " --> pdb=" O   LYS A 547 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 610
      Proline residue:  A 604  - end of helix
    Processing helix  chain 'A' and resid 611 through 631
    Processing helix  chain 'A' and resid 653 through 665
      removed outlier: 3.595A  pdb=" N   TRP A 665 " --> pdb=" O   ALA A 661 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 688 through 698
    Processing helix  chain 'A' and resid 710 through 720
      removed outlier: 3.773A  pdb=" N   LEU A 720 " --> pdb=" O   ARG A 716 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 728 through 733
      removed outlier: 3.578A  pdb=" N   VAL A 732 " --> pdb=" O   ASP A 728 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 739 through 756
    Processing helix  chain 'A' and resid 766 through 776
      removed outlier: 3.554A  pdb=" N   PHE A 770 " --> pdb=" O   THR A 766 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 795 through 800
      removed outlier: 4.210A  pdb=" N   SER A 800 " --> pdb=" O   PRO A 796 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 21 through 29
    Processing helix  chain 'B' and resid 46 through 54
    Processing helix  chain 'B' and resid 56 through 61
      removed outlier: 4.119A  pdb=" N   ILE B  61 " --> pdb=" O   ARG B  57 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 75 through 88
      removed outlier: 4.359A  pdb=" N   GLU B  79 " --> pdb=" O   PRO B  75 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 149
      removed outlier: 4.250A  pdb=" N   ALA B 138 " --> pdb=" O   SER B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 170 through 178
    Processing helix  chain 'B' and resid 180 through 185
    Processing helix  chain 'B' and resid 188 through 193
    Processing helix  chain 'B' and resid 200 through 212
      removed outlier: 4.618A  pdb=" N   LEU B 206 " --> pdb=" O   ASN B 202 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   GLN B 207 " --> pdb=" O   ARG B 203 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 258 through 274
    Processing helix  chain 'B' and resid 278 through 294
    Processing helix  chain 'B' and resid 352 through 378
    Processing helix  chain 'B' and resid 394 through 407
    Processing helix  chain 'B' and resid 422 through 430
    Processing helix  chain 'B' and resid 430 through 448
      removed outlier: 3.619A  pdb=" N   ALA B 434 " --> pdb=" O   GLY B 430 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   GLN B 436 " --> pdb=" O   ALA B 432 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   LYS B 448 " --> pdb=" O   ARG B 444 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 471 through 486
      removed outlier: 4.142A  pdb=" N   VAL B 486 " --> pdb=" O   LEU B 482 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 512 through 531
      removed outlier: 3.581A  pdb=" N   LEU B 516 " --> pdb=" O   ASN B 512 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 539 through 562
      removed outlier: 4.133A  pdb=" N   LYS B 547 " --> pdb=" O   ASN B 543 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 598 through 610
      Proline residue:  B 604  - end of helix
    Processing helix  chain 'B' and resid 611 through 634
      removed outlier: 3.856A  pdb=" N   ILE B 615 " --> pdb=" O   GLU B 611 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   GLN B 633 " --> pdb=" O   GLU B 629 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 653 through 665
      removed outlier: 4.413A  pdb=" N   ALA B 661 " --> pdb=" O   GLN B 657 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 678 through 683
      removed outlier: 3.802A  pdb=" N   MET B 682 " --> pdb=" O   GLU B 678 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 686 through 699
      removed outlier: 3.955A  pdb=" N   LYS B 690 " --> pdb=" O   THR B 686 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   LEU B 695 " --> pdb=" O   ARG B 691 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 709 through 720
      removed outlier: 3.692A  pdb=" N   GLY B 713 " --> pdb=" O   THR B 709 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 728 through 733
    Processing helix  chain 'B' and resid 738 through 755
    Processing helix  chain 'B' and resid 766 through 776
      removed outlier: 3.942A  pdb=" N   PHE B 770 " --> pdb=" O   THR B 766 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 794 through 802
    Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 36
    Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 168
      removed outlier: 3.908A  pdb=" N   GLN A 168 " --> pdb=" O   VAL A 159 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 219 through 223
    Processing sheet with id=AA4, first strand: chain 'A' and resid 308 through 314
      removed outlier: 6.858A  pdb=" N   LEU A 301 " --> pdb=" O   TRP A 312 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   SER A 314 " --> pdb=" O   VAL A 299 " (cutoff:3.500A)
      removed outlier: 7.043A  pdb=" N   VAL A 299 " --> pdb=" O   SER A 314 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   ALA A 339 " --> pdb=" O   LEU A 304 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 308 through 314
      removed outlier: 6.858A  pdb=" N   LEU A 301 " --> pdb=" O   TRP A 312 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   SER A 314 " --> pdb=" O   VAL A 299 " (cutoff:3.500A)
      removed outlier: 7.043A  pdb=" N   VAL A 299 " --> pdb=" O   SER A 314 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   ALA A 339 " --> pdb=" O   LEU A 304 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   ILE A 331 " --> pdb=" O   ALA A 339 " (cutoff:3.500A)
      removed outlier: 4.533A  pdb=" N   ILE A 341 " --> pdb=" O   ALA A 329 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   ALA A 329 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 454 through 459
      removed outlier: 3.669A  pdb=" N   ILE A 458 " --> pdb=" O   GLN A 462 " (cutoff:3.500A)
      removed outlier: 7.171A  pdb=" N   GLN A 462 " --> pdb=" O   ILE A 458 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 490 through 491
    Processing sheet with id=AA8, first strand: chain 'A' and resid 595 through 597
      removed outlier: 3.997A  pdb=" N   TRP A 589 " --> pdb=" O   VAL A 597 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   LEU A 580 " --> pdb=" O   PHE A 574 " (cutoff:3.500A)
      removed outlier: 5.852A  pdb=" N   PHE A 574 " --> pdb=" O   LEU A 580 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 595 through 597
      removed outlier: 3.997A  pdb=" N   TRP A 589 " --> pdb=" O   VAL A 597 " (cutoff:3.500A)
      removed outlier: 4.712A  pdb=" N   ASN A 643 " --> pdb=" O   ALA A 585 " (cutoff:3.500A)
      removed outlier: 8.295A  pdb=" N   ALA A 587 " --> pdb=" O   ASN A 643 " (cutoff:3.500A)
      removed outlier: 6.380A  pdb=" N   LEU A 640 " --> pdb=" O   THR A 673 " (cutoff:3.500A)
      removed outlier: 7.821A  pdb=" N   GLU A 675 " --> pdb=" O   LEU A 640 " (cutoff:3.500A)
      removed outlier: 7.104A  pdb=" N   VAL A 642 " --> pdb=" O   GLU A 675 " (cutoff:3.500A)
      removed outlier: 7.144A  pdb=" N   LEU A 672 " --> pdb=" O   GLY A 701 " (cutoff:3.500A)
      removed outlier: 8.444A  pdb=" N   SER A 703 " --> pdb=" O   LEU A 672 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   VAL A 674 " --> pdb=" O   SER A 703 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   LEU A 702 " --> pdb=" O   GLU A 724 " (cutoff:3.500A)
      removed outlier: 7.836A  pdb=" N   LYS A 726 " --> pdb=" O   LEU A 702 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   VAL A 704 " --> pdb=" O   LYS A 726 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   ILE A 725 " --> pdb=" O   VAL A 760 " (cutoff:3.500A)
      removed outlier: 7.734A  pdb=" N   GLU A 762 " --> pdb=" O   ILE A 725 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   ILE A 727 " --> pdb=" O   GLU A 762 " (cutoff:3.500A)
      removed outlier: 7.046A  pdb=" N   VAL A 759 " --> pdb=" O   VAL A 780 " (cutoff:3.500A)
      removed outlier: 8.230A  pdb=" N   GLN A 782 " --> pdb=" O   VAL A 759 " (cutoff:3.500A)
      removed outlier: 6.041A  pdb=" N   ALA A 761 " --> pdb=" O   GLN A 782 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 42 through 45
      removed outlier: 3.999A  pdb=" N   PHE B  44 " --> pdb=" O   LEU B  35 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 166 through 169
      removed outlier: 6.817A  pdb=" N   VAL B 159 " --> pdb=" O   VAL B 167 " (cutoff:3.500A)
      removed outlier: 4.929A  pdb=" N   CYS B 169 " --> pdb=" O   VAL B 157 " (cutoff:3.500A)
      removed outlier: 7.581A  pdb=" N   VAL B 157 " --> pdb=" O   CYS B 169 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 308 through 314
      removed outlier: 6.948A  pdb=" N   LEU B 301 " --> pdb=" O   TRP B 312 " (cutoff:3.500A)
      removed outlier: 4.907A  pdb=" N   SER B 314 " --> pdb=" O   VAL B 299 " (cutoff:3.500A)
      removed outlier: 7.257A  pdb=" N   VAL B 299 " --> pdb=" O   SER B 314 " (cutoff:3.500A)
      removed outlier: 7.266A  pdb=" N   ALA B 339 " --> pdb=" O   LEU B 304 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   GLY B 340 " --> pdb=" O   ILE B 331 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 454 through 457
    Processing sheet with id=AB5, first strand: chain 'B' and resid 490 through 491
      removed outlier: 3.631A  pdb=" N   ILE B 490 " --> pdb=" O   PHE B 497 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   PHE B 497 " --> pdb=" O   ILE B 490 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'B' and resid 595 through 597
      removed outlier: 4.387A  pdb=" N   TRP B 589 " --> pdb=" O   VAL B 597 " (cutoff:3.500A)
      removed outlier: 4.714A  pdb=" N   ASN B 643 " --> pdb=" O   ALA B 585 " (cutoff:3.500A)
      removed outlier: 7.857A  pdb=" N   ALA B 587 " --> pdb=" O   ASN B 643 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 595 through 597
      removed outlier: 4.387A  pdb=" N   TRP B 589 " --> pdb=" O   VAL B 597 " (cutoff:3.500A)
      removed outlier: 7.082A  pdb=" N   LEU B 580 " --> pdb=" O   PHE B 574 " (cutoff:3.500A)
      removed outlier: 6.220A  pdb=" N   PHE B 574 " --> pdb=" O   LEU B 580 " (cutoff:3.500A)
      removed outlier: 4.803A  pdb=" N   GLY B 783 " --> pdb=" O   PRO B 571 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   VAL B 759 " --> pdb=" O   VAL B 780 " (cutoff:3.500A)
      removed outlier: 7.857A  pdb=" N   GLN B 782 " --> pdb=" O   VAL B 759 " (cutoff:3.500A)
      removed outlier: 5.839A  pdb=" N   ALA B 761 " --> pdb=" O   GLN B 782 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   ILE B 725 " --> pdb=" O   VAL B 760 " (cutoff:3.500A)
      removed outlier: 8.033A  pdb=" N   GLU B 762 " --> pdb=" O   ILE B 725 " (cutoff:3.500A)
      removed outlier: 7.149A  pdb=" N   ILE B 727 " --> pdb=" O   GLU B 762 " (cutoff:3.500A)
      removed outlier: 8.160A  pdb=" N   VAL B 764 " --> pdb=" O   ILE B 727 " (cutoff:3.500A)

    691 hydrogen bonds defined for protein.
    1971 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.86

  Time building geometry restraints manager: 3.70 seconds

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

  Histogram of bond lengths:
        1.22 -     1.38: 4990
        1.38 -     1.54: 7670
        1.54 -     1.70: 46
        1.70 -     1.87: 116
        1.87 -     2.03: 8
  Bond restraints: 12830
  Sorted by residual:
  bond pdb=" N   MET B 273 "
       pdb=" CA  MET B 273 "
    ideal  model  delta    sigma   weight residual
    1.457  1.484 -0.027 1.32e-02 5.74e+03 4.23e+00
  bond pdb=" CG1 ILE B 285 "
       pdb=" CD1 ILE B 285 "
    ideal  model  delta    sigma   weight residual
    1.513  1.435  0.078 3.90e-02 6.57e+02 3.97e+00
  bond pdb=" CB  VAL A 597 "
       pdb=" CG2 VAL A 597 "
    ideal  model  delta    sigma   weight residual
    1.521  1.461  0.060 3.30e-02 9.18e+02 3.35e+00
  bond pdb=" C   ASP A 387 "
       pdb=" N   PRO A 388 "
    ideal  model  delta    sigma   weight residual
    1.337  1.317  0.019 1.11e-02 8.12e+03 3.01e+00
  bond pdb=" CA  GLN A 385 "
       pdb=" CB  GLN A 385 "
    ideal  model  delta    sigma   weight residual
    1.530  1.556 -0.026 1.69e-02 3.50e+03 2.34e+00
  ... (remaining 12825 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.40: 17009
        2.40 -     4.81: 329
        4.81 -     7.21: 52
        7.21 -     9.61: 15
        9.61 -    12.01: 7
  Bond angle restraints: 17412
  Sorted by residual:
  angle pdb=" C   ALA B 272 "
        pdb=" N   MET B 273 "
        pdb=" CA  MET B 273 "
      ideal   model   delta    sigma   weight residual
     121.94  110.14   11.80 2.00e+00 2.50e-01 3.48e+01
  angle pdb=" N   ARG A 779 "
        pdb=" CA  ARG A 779 "
        pdb=" CB  ARG A 779 "
      ideal   model   delta    sigma   weight residual
     114.17  108.08    6.09 1.14e+00 7.69e-01 2.86e+01
  angle pdb=" C   ASN B  64 "
        pdb=" CA  ASN B  64 "
        pdb=" CB  ASN B  64 "
      ideal   model   delta    sigma   weight residual
     117.23  110.49    6.74 1.36e+00 5.41e-01 2.46e+01
  angle pdb=" C   GLN B 385 "
        pdb=" CA  GLN B 385 "
        pdb=" CB  GLN B 385 "
      ideal   model   delta    sigma   weight residual
     109.16  115.48   -6.32 1.29e+00 6.01e-01 2.40e+01
  angle pdb=" CA  GLN B 385 "
        pdb=" CB  GLN B 385 "
        pdb=" CG  GLN B 385 "
      ideal   model   delta    sigma   weight residual
     114.10  123.72   -9.62 2.00e+00 2.50e-01 2.31e+01
  ... (remaining 17407 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 6683
       17.92 -    35.84: 819
       35.84 -    53.76: 202
       53.76 -    71.68: 32
       71.68 -    89.60: 16
  Dihedral angle restraints: 7752
    sinusoidal: 3190
      harmonic: 4562
  Sorted by residual:
  dihedral pdb=" CA  LEU A 294 "
           pdb=" C   LEU A 294 "
           pdb=" N   ASN A 295 "
           pdb=" CA  ASN A 295 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.15  -21.85     0      5.00e+00 4.00e-02 1.91e+01
  dihedral pdb=" CA  HIS A  77 "
           pdb=" C   HIS A  77 "
           pdb=" N   PRO A  78 "
           pdb=" CA  PRO A  78 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.07  -20.93     0      5.00e+00 4.00e-02 1.75e+01
  dihedral pdb=" CA  VAL B 150 "
           pdb=" C   VAL B 150 "
           pdb=" N   ASP B 151 "
           pdb=" CA  ASP B 151 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.38  -19.62     0      5.00e+00 4.00e-02 1.54e+01
  ... (remaining 7749 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.092: 1790
       0.092 -    0.183: 135
       0.183 -    0.275: 1
       0.275 -    0.366: 0
       0.366 -    0.458: 1
  Chirality restraints: 1927
  Sorted by residual:
  chirality pdb=" CG  LEU A 550 "
            pdb=" CB  LEU A 550 "
            pdb=" CD1 LEU A 550 "
            pdb=" CD2 LEU A 550 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.13   -0.46 2.00e-01 2.50e+01 5.23e+00
  chirality pdb=" CB  ILE B 285 "
            pdb=" CA  ILE B 285 "
            pdb=" CG1 ILE B 285 "
            pdb=" CG2 ILE B 285 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.26 2.00e-01 2.50e+01 1.69e+00
  chirality pdb=" CA  PHE B 707 "
            pdb=" N   PHE B 707 "
            pdb=" C   PHE B 707 "
            pdb=" CB  PHE B 707 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.24e-01
  ... (remaining 1924 not shown)

  Planarity restraints: 2265
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 452 "   -0.016 2.00e-02 2.50e+03   3.10e-02 9.63e+00
        pdb=" C   ASP B 452 "    0.054 2.00e-02 2.50e+03
        pdb=" O   ASP B 452 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   GLN B 453 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B 570 "   -0.043 5.00e-02 4.00e+02   6.51e-02 6.79e+00
        pdb=" N   PRO B 571 "    0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO B 571 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO B 571 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 779 "   -0.011 2.00e-02 2.50e+03   2.12e-02 4.48e+00
        pdb=" C   ARG A 779 "    0.037 2.00e-02 2.50e+03
        pdb=" O   ARG A 779 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   VAL A 780 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 2262 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 190
        2.63 -     3.20: 11769
        3.20 -     3.77: 19943
        3.77 -     4.33: 26293
        4.33 -     4.90: 42366
  Nonbonded interactions: 100561
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 394 "
            pdb=" N   ARG A 395 "
     model   vdw
     2.064 3.120
  nonbonded pdb=" OG  SER A 632 "
            pdb=" OE1 GLN A 633 "
     model   vdw
     2.195 3.040
  nonbonded pdb=" O   PRO A  78 "
            pdb=" NH1 ARG A  82 "
     model   vdw
     2.213 3.120
  nonbonded pdb=" OD1 ASP B  66 "
            pdb=" NH1 ARG B  74 "
     model   vdw
     2.216 3.120
  nonbonded pdb=" O   GLY A 336 "
            pdb=" NH2 ARG B 205 "
     model   vdw
     2.231 3.120
  ... (remaining 100556 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 20 through 378 or resid 384 through 807 or resid 901))
  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:             2.850
  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:          0.490
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     32.710
  Find NCS groups from input model:        0.550
  Set up NCS constraints:                  0.060
  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:3.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
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      :  0.006   0.215  12831  Z= 0.244
  Angle     :  0.839  12.013  17412  Z= 0.440
  Chirality :  0.049   0.458   1927
  Planarity :  0.005   0.065   2265
  Dihedral  : 16.685  89.602   4790
  Min Nonbonded Distance : 2.064

Molprobity Statistics.
  All-atom Clashscore : 17.52
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.13 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  : 25.86 %
    Favored  : 73.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    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: -0.45 (0.21), residues: 1565
  helix:  0.57 (0.20), residues: 669
  sheet: -0.12 (0.28), residues: 321
  loop : -1.37 (0.26), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 231 
 HIS   0.009   0.001   HIS A 165 
 PHE   0.033   0.003   PHE A 602 
 TYR   0.024   0.002   TYR B 581 
 ARG   0.015   0.001   ARG A 788 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12721 (  671)
  hydrogen bonds       : angle       6.31800 ( 1971)
  covalent geometry    : bond        0.00568 (12830)
  covalent geometry    : angle       0.83930 (17412)
  Misc. bond           : bond        0.21513 (    1)

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

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

  3130 Ramachandran restraints generated.
    1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3130 Ramachandran restraints generated.
    1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 210
  time to evaluate  : 1.555 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  273 MET cc_start: 0.7526 (tpt) cc_final: 0.7304 (tpt)
REVERT: A  491 MET cc_start: 0.8634 (tpp) cc_final: 0.8425 (tpp)
  outliers start: 6
  outliers final: 2
  residues processed: 216
  average time/residue: 0.2929
  time to fit residues: 87.3404
Evaluate side-chains
  119 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 117
  time to evaluate  : 1.659 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  678 GLU
Chi-restraints excluded: chain B residue   22 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 131 optimal weight:    1.9990
   chunk 118 optimal weight:    0.8980
   chunk 65 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9980
   chunk 79 optimal weight:    7.9990
   chunk 63 optimal weight:    3.9990
   chunk 122 optimal weight:    0.5980
   chunk 47 optimal weight:    4.9990
   chunk 74 optimal weight:    2.9990
   chunk 91 optimal weight:    0.6980
   chunk 141 optimal weight:    2.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 100 GLN
** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 325 GLN
** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 633 GLN
** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  39 ASN
** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 245 HIS
B 289 ASN
** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.075242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.055734 restraints weight = 62774.349|
|-----------------------------------------------------------------------------|
r_work (start): 0.3335 rms_B_bonded: 5.90
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.2140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.091  12831  Z= 0.169
  Angle     :  0.746  10.275  17412  Z= 0.375
  Chirality :  0.046   0.364   1927
  Planarity :  0.005   0.060   2265
  Dihedral  :  6.213  77.759   1715
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 14.81
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.24 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 23.29 %
    Favored  : 73.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    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: -0.07 (0.21), residues: 1565
  helix:  0.90 (0.20), residues: 687
  sheet: -0.03 (0.28), residues: 314
  loop : -1.16 (0.27), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 312 
 HIS   0.006   0.001   HIS B 245 
 PHE   0.026   0.002   PHE A 602 
 TYR   0.017   0.001   TYR B 581 
 ARG   0.007   0.001   ARG A 788 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04023 (  671)
  hydrogen bonds       : angle       5.23030 ( 1971)
  covalent geometry    : bond        0.00379 (12830)
  covalent geometry    : angle       0.74582 (17412)
  Misc. bond           : bond        0.09081 (    1)

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

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

  3130 Ramachandran restraints generated.
    1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3130 Ramachandran restraints generated.
    1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 122
  time to evaluate  : 1.600 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.7988 (p0)
REVERT: A  217 GLN cc_start: 0.9002 (pp30) cc_final: 0.8795 (pp30)
REVERT: A  286 ILE cc_start: 0.8659 (mt) cc_final: 0.8396 (mt)
REVERT: A  550 LEU cc_start: 0.9226 (mm) cc_final: 0.8972 (pp)
REVERT: A  607 GLU cc_start: 0.9027 (mm-30) cc_final: 0.8756 (mm-30)
REVERT: A  698 MET cc_start: 0.8929 (mtm) cc_final: 0.8662 (mtm)
REVERT: A  702 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8628 (mm)
REVERT: B  151 ASP cc_start: 0.7916 (m-30) cc_final: 0.7516 (m-30)
REVERT: B  251 MET cc_start: 0.8507 (mtp) cc_final: 0.8284 (mtp)
REVERT: B  273 MET cc_start: 0.8559 (pmm) cc_final: 0.8281 (pmm)
REVERT: B  424 ASP cc_start: 0.9235 (m-30) cc_final: 0.8919 (t0)
REVERT: B  542 MET cc_start: 0.8748 (ppp) cc_final: 0.8379 (ppp)
REVERT: B  545 MET cc_start: 0.8393 (tmm) cc_final: 0.8112 (tmm)
REVERT: B  640 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8405 (tp)
REVERT: B  680 MET cc_start: 0.9104 (ttp) cc_final: 0.8541 (ptm)
REVERT: B  806 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7951 (tppt)
  outliers start: 41
  outliers final: 18
  residues processed: 154
  average time/residue: 0.2356
  time to fit residues: 54.5870
Evaluate side-chains
  125 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 103
  time to evaluate  : 1.585 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 HIS
Chi-restraints excluded: chain A residue  126 TYR
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  161 ASP
Chi-restraints excluded: chain A residue  180 CYS
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  389 MET
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  603 ILE
Chi-restraints excluded: chain A residue  702 LEU
Chi-restraints excluded: chain A residue  806 LYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  145 GLN
Chi-restraints excluded: chain B residue  181 ILE
Chi-restraints excluded: chain B residue  270 LEU
Chi-restraints excluded: chain B residue  299 VAL
Chi-restraints excluded: chain B residue  640 LEU
Chi-restraints excluded: chain B residue  685 ASP
Chi-restraints excluded: chain B residue  700 VAL
Chi-restraints excluded: chain B residue  759 VAL
Chi-restraints excluded: chain B residue  806 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 145 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9990
   chunk 104 optimal weight:    0.8980
   chunk 68 optimal weight:    6.9990
   chunk 51 optimal weight:    0.7980
   chunk 22 optimal weight:    5.9990
   chunk 155 optimal weight:    0.9980
   chunk 92 optimal weight:    0.5980
   chunk 47 optimal weight:    0.0970
   chunk 120 optimal weight:    0.0870
   overall best weight:    0.4956

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

Flipped N/Q/H residues before XYZ refinement:
** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.071674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.053542 restraints weight = 70346.114|
|-----------------------------------------------------------------------------|
r_work (start): 0.3344 rms_B_bonded: 6.05
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.2631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064  12831  Z= 0.128
  Angle     :  0.677   9.872  17412  Z= 0.335
  Chirality :  0.044   0.274   1927
  Planarity :  0.005   0.057   2265
  Dihedral  :  5.992  77.262   1710
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 12.65
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.11 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 21.31 %
    Favored  : 76.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    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:  0.10 (0.22), residues: 1565
  helix:  1.00 (0.20), residues: 704
  sheet:  0.05 (0.29), residues: 312
  loop : -1.06 (0.28), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.001   TRP B 312 
 HIS   0.005   0.001   HIS B 663 
 PHE   0.024   0.002   PHE A 602 
 TYR   0.015   0.001   TYR B 581 
 ARG   0.004   0.000   ARG A 740 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03502 (  671)
  hydrogen bonds       : angle       4.88924 ( 1971)
  covalent geometry    : bond        0.00296 (12830)
  covalent geometry    : angle       0.67657 (17412)
  Misc. bond           : bond        0.06394 (    1)

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

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

  3130 Ramachandran restraints generated.
    1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3130 Ramachandran restraints generated.
    1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 114
  time to evaluate  : 1.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 MET cc_start: 0.6990 (tpp) cc_final: 0.6363 (tpp)
REVERT: A   95 MET cc_start: 0.8920 (mmm) cc_final: 0.8696 (mmm)
REVERT: A  137 MET cc_start: 0.8723 (ttm) cc_final: 0.8507 (ttm)
REVERT: A  217 GLN cc_start: 0.8970 (pp30) cc_final: 0.8646 (pp30)
REVERT: A  477 GLN cc_start: 0.8391 (pp30) cc_final: 0.8173 (pp30)
REVERT: A  480 ASP cc_start: 0.8926 (m-30) cc_final: 0.8707 (m-30)
REVERT: A  702 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8520 (mm)
REVERT: B   95 MET cc_start: 0.6135 (mpp) cc_final: 0.4572 (mpp)
REVERT: B  284 GLU cc_start: 0.9314 (OUTLIER) cc_final: 0.9048 (tt0)
REVERT: B  424 ASP cc_start: 0.9303 (m-30) cc_final: 0.8983 (t0)
REVERT: B  542 MET cc_start: 0.8683 (ppp) cc_final: 0.8078 (ppp)
REVERT: B  640 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8393 (tp)
REVERT: B  680 MET cc_start: 0.9179 (ttp) cc_final: 0.8517 (ptm)
REVERT: B  772 MET cc_start: 0.8255 (ppp) cc_final: 0.8013 (ppp)
REVERT: B  806 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7975 (tppt)
  outliers start: 35
  outliers final: 18
  residues processed: 138
  average time/residue: 0.2148
  time to fit residues: 45.3931
Evaluate side-chains
  121 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 99
  time to evaluate  : 1.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 HIS
Chi-restraints excluded: chain A residue   83 HIS
Chi-restraints excluded: chain A residue  126 TYR
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  232 ILE
Chi-restraints excluded: chain A residue  389 MET
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  407 ASP
Chi-restraints excluded: chain A residue  524 MET
Chi-restraints excluded: chain A residue  597 VAL
Chi-restraints excluded: chain A residue  702 LEU
Chi-restraints excluded: chain A residue  725 ILE
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  181 ILE
Chi-restraints excluded: chain B residue  270 LEU
Chi-restraints excluded: chain B residue  284 GLU
Chi-restraints excluded: chain B residue  299 VAL
Chi-restraints excluded: chain B residue  640 LEU
Chi-restraints excluded: chain B residue  685 ASP
Chi-restraints excluded: chain B residue  759 VAL
Chi-restraints excluded: chain B residue  806 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 105 optimal weight:    4.9990
   chunk 147 optimal weight:    0.9990
   chunk 30 optimal weight:    9.9990
   chunk 34 optimal weight:    0.7980
   chunk 94 optimal weight:    0.9980
   chunk 150 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 61 optimal weight:    0.2980
   chunk 76 optimal weight:    0.7980
   chunk 116 optimal weight:    1.9990
   chunk 151 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 142 GLN
A 311 HIS
** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 653 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 = 0.3889 r_free = 0.3889 target = 0.070989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.052941 restraints weight = 69915.321|
|-----------------------------------------------------------------------------|
r_work (start): 0.3330 rms_B_bonded: 6.37
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.2938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062  12831  Z= 0.138
  Angle     :  0.647  10.083  17412  Z= 0.322
  Chirality :  0.043   0.169   1927
  Planarity :  0.004   0.058   2265
  Dihedral  :  5.962  77.446   1710
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 12.21
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.18 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 22.34 %
    Favored  : 74.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    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:  0.21 (0.22), residues: 1565
  helix:  1.09 (0.20), residues: 706
  sheet:  0.05 (0.29), residues: 312
  loop : -0.98 (0.28), residues: 547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.002   TRP B 312 
 HIS   0.006   0.001   HIS A 245 
 PHE   0.024   0.002   PHE A 602 
 TYR   0.018   0.001   TYR B 581 
 ARG   0.003   0.000   ARG B 288 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03251 (  671)
  hydrogen bonds       : angle       4.75625 ( 1971)
  covalent geometry    : bond        0.00327 (12830)
  covalent geometry    : angle       0.64702 (17412)
  Misc. bond           : bond        0.06183 (    1)

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

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

  3130 Ramachandran restraints generated.
    1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3130 Ramachandran restraints generated.
    1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 104
  time to evaluate  : 1.437 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 MET cc_start: 0.6832 (tpp) cc_final: 0.6178 (tpp)
REVERT: A  161 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.8091 (p0)
REVERT: A  167 VAL cc_start: 0.7175 (OUTLIER) cc_final: 0.6856 (p)
REVERT: A  176 MET cc_start: 0.7716 (tpp) cc_final: 0.7436 (tpp)
REVERT: A  480 ASP cc_start: 0.8858 (m-30) cc_final: 0.8637 (m-30)
REVERT: B  273 MET cc_start: 0.8832 (pmm) cc_final: 0.8505 (pmm)
REVERT: B  416 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7419 (tt)
REVERT: B  424 ASP cc_start: 0.9359 (m-30) cc_final: 0.9037 (t0)
REVERT: B  542 MET cc_start: 0.8494 (ppp) cc_final: 0.8188 (ppp)
REVERT: B  640 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8373 (tp)
REVERT: B  680 MET cc_start: 0.9078 (ttp) cc_final: 0.8405 (ptm)
REVERT: B  772 MET cc_start: 0.8332 (ppp) cc_final: 0.8047 (ppp)
REVERT: B  806 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7981 (tppt)
  outliers start: 41
  outliers final: 27
  residues processed: 136
  average time/residue: 0.2385
  time to fit residues: 49.2197
Evaluate side-chains
  130 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 98
  time to evaluate  : 1.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 MET
Chi-restraints excluded: chain A residue   77 HIS
Chi-restraints excluded: chain A residue   83 HIS
Chi-restraints excluded: chain A residue  126 TYR
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  161 ASP
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  232 ILE
Chi-restraints excluded: chain A residue  286 ILE
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  407 ASP
Chi-restraints excluded: chain A residue  524 MET
Chi-restraints excluded: chain A residue  603 ILE
Chi-restraints excluded: chain A residue  631 ARG
Chi-restraints excluded: chain A residue  702 LEU
Chi-restraints excluded: chain A residue  725 ILE
Chi-restraints excluded: chain B residue   22 PHE
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  181 ILE
Chi-restraints excluded: chain B residue  270 LEU
Chi-restraints excluded: chain B residue  299 VAL
Chi-restraints excluded: chain B residue  416 LEU
Chi-restraints excluded: chain B residue  597 VAL
Chi-restraints excluded: chain B residue  640 LEU
Chi-restraints excluded: chain B residue  685 ASP
Chi-restraints excluded: chain B residue  700 VAL
Chi-restraints excluded: chain B residue  717 LEU
Chi-restraints excluded: chain B residue  759 VAL
Chi-restraints excluded: chain B residue  806 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 79 optimal weight:   10.0000
   chunk 16 optimal weight:    3.9990
   chunk 23 optimal weight:    0.8980
   chunk 153 optimal weight:    1.9990
   chunk 30 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9990
   chunk 105 optimal weight:    3.9990
   chunk 4 optimal weight:    0.6980
   chunk 128 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 140 optimal weight:    2.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 399 HIS
** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  84 ASN
** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 653 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 = 0.3869 r_free = 0.3869 target = 0.070038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.051193 restraints weight = 70850.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.3290 rms_B_bonded: 5.72
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.3181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  12831  Z= 0.160
  Angle     :  0.651   9.781  17412  Z= 0.323
  Chirality :  0.043   0.164   1927
  Planarity :  0.004   0.059   2265
  Dihedral  :  6.021  76.786   1710
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 12.33
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.37 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 22.56 %
    Favored  : 73.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    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:  0.23 (0.22), residues: 1565
  helix:  1.10 (0.20), residues: 706
  sheet: -0.04 (0.29), residues: 312
  loop : -0.89 (0.28), residues: 547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B 312 
 HIS   0.004   0.001   HIS A 521 
 PHE   0.026   0.002   PHE A 602 
 TYR   0.019   0.001   TYR B 581 
 ARG   0.003   0.000   ARG A 164 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03222 (  671)
  hydrogen bonds       : angle       4.73482 ( 1971)
  covalent geometry    : bond        0.00379 (12830)
  covalent geometry    : angle       0.65146 (17412)
  Misc. bond           : bond        0.05362 (    1)

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

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

  3130 Ramachandran restraints generated.
    1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3130 Ramachandran restraints generated.
    1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 102
  time to evaluate  : 2.113 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 MET cc_start: 0.6842 (tpp) cc_final: 0.6228 (tpp)
REVERT: A   99 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7583 (mm)
REVERT: A  167 VAL cc_start: 0.7314 (OUTLIER) cc_final: 0.7042 (p)
REVERT: A  176 MET cc_start: 0.7823 (tpp) cc_final: 0.7538 (tpp)
REVERT: A  187 MET cc_start: 0.8674 (ppp) cc_final: 0.8012 (ppp)
REVERT: A  480 ASP cc_start: 0.8994 (m-30) cc_final: 0.8752 (m-30)
REVERT: B   43 MET cc_start: 0.8483 (mpp) cc_final: 0.8244 (mpp)
REVERT: B   95 MET cc_start: 0.6189 (mpp) cc_final: 0.4312 (mpp)
REVERT: B  273 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8274 (pmm)
REVERT: B  424 ASP cc_start: 0.9401 (m-30) cc_final: 0.9073 (t0)
REVERT: B  640 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8298 (tp)
REVERT: B  680 MET cc_start: 0.9118 (ttp) cc_final: 0.8355 (ptm)
REVERT: B  772 MET cc_start: 0.8440 (ppp) cc_final: 0.8132 (ppp)
REVERT: B  806 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7877 (tppt)
  outliers start: 52
  outliers final: 30
  residues processed: 143
  average time/residue: 0.2655
  time to fit residues: 57.1958
Evaluate side-chains
  130 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 95
  time to evaluate  : 1.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 MET
Chi-restraints excluded: chain A residue   77 HIS
Chi-restraints excluded: chain A residue   83 HIS
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  126 TYR
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  180 CYS
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  232 ILE
Chi-restraints excluded: chain A residue  286 ILE
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  389 MET
Chi-restraints excluded: chain A residue  407 ASP
Chi-restraints excluded: chain A residue  524 MET
Chi-restraints excluded: chain A residue  603 ILE
Chi-restraints excluded: chain A residue  631 ARG
Chi-restraints excluded: chain A residue  725 ILE
Chi-restraints excluded: chain B residue   22 PHE
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  181 ILE
Chi-restraints excluded: chain B residue  270 LEU
Chi-restraints excluded: chain B residue  273 MET
Chi-restraints excluded: chain B residue  279 PHE
Chi-restraints excluded: chain B residue  299 VAL
Chi-restraints excluded: chain B residue  456 CYS
Chi-restraints excluded: chain B residue  597 VAL
Chi-restraints excluded: chain B residue  640 LEU
Chi-restraints excluded: chain B residue  641 SER
Chi-restraints excluded: chain B residue  685 ASP
Chi-restraints excluded: chain B residue  717 LEU
Chi-restraints excluded: chain B residue  759 VAL
Chi-restraints excluded: chain B residue  766 THR
Chi-restraints excluded: chain B residue  806 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 1 optimal weight:   10.0000
   chunk 2 optimal weight:    9.9990
   chunk 83 optimal weight:   10.0000
   chunk 121 optimal weight:    0.0870
   chunk 0 optimal weight:    9.9990
   chunk 151 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 136 optimal weight:    0.7980
   chunk 154 optimal weight:    0.7980
   chunk 128 optimal weight:    0.4980
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 477 GLN
** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 142 GLN
B 165 HIS
B 245 HIS
** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.073871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.054376 restraints weight = 64239.486|
|-----------------------------------------------------------------------------|
r_work (start): 0.3317 rms_B_bonded: 5.87
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.3439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.213  12831  Z= 0.124
  Angle     :  0.648  10.984  17412  Z= 0.315
  Chirality :  0.043   0.165   1927
  Planarity :  0.004   0.062   2265
  Dihedral  :  5.983  77.627   1710
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 11.65
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.05 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 23.81 %
    Favored  : 72.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    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:  0.31 (0.22), residues: 1565
  helix:  1.17 (0.20), residues: 707
  sheet: -0.02 (0.29), residues: 310
  loop : -0.85 (0.28), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP B 312 
 HIS   0.008   0.001   HIS B 245 
 PHE   0.023   0.001   PHE A 602 
 TYR   0.016   0.001   TYR B 581 
 ARG   0.003   0.000   ARG B 288 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03036 (  671)
  hydrogen bonds       : angle       4.59236 ( 1971)
  covalent geometry    : bond        0.00291 (12830)
  covalent geometry    : angle       0.64827 (17412)
  Misc. bond           : bond        0.21289 (    1)

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

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

  3130 Ramachandran restraints generated.
    1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3130 Ramachandran restraints generated.
    1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 99
  time to evaluate  : 2.161 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 MET cc_start: 0.6879 (tpp) cc_final: 0.6216 (tpp)
REVERT: A   99 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.7900 (mm)
REVERT: A  159 VAL cc_start: 0.7707 (OUTLIER) cc_final: 0.7482 (t)
REVERT: A  161 ASP cc_start: 0.8414 (OUTLIER) cc_final: 0.7993 (p0)
REVERT: A  176 MET cc_start: 0.7807 (tpp) cc_final: 0.7520 (tpp)
REVERT: A  480 ASP cc_start: 0.9014 (m-30) cc_final: 0.8755 (m-30)
REVERT: A  702 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8602 (mm)
REVERT: B   43 MET cc_start: 0.8106 (mpp) cc_final: 0.7802 (mpp)
REVERT: B   95 MET cc_start: 0.6619 (mpp) cc_final: 0.5116 (mpp)
REVERT: B  273 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.8130 (pmm)
REVERT: B  424 ASP cc_start: 0.9275 (m-30) cc_final: 0.8990 (t0)
REVERT: B  494 ASP cc_start: 0.9266 (p0) cc_final: 0.9005 (p0)
REVERT: B  542 MET cc_start: 0.8466 (ppp) cc_final: 0.7024 (ppp)
REVERT: B  545 MET cc_start: 0.8100 (tmm) cc_final: 0.7509 (ppp)
REVERT: B  680 MET cc_start: 0.9095 (ttp) cc_final: 0.8388 (ptm)
REVERT: B  772 MET cc_start: 0.8414 (ppp) cc_final: 0.8111 (ppp)
REVERT: B  806 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7962 (mmmt)
  outliers start: 45
  outliers final: 27
  residues processed: 136
  average time/residue: 0.2530
  time to fit residues: 52.1712
Evaluate side-chains
  124 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 91
  time to evaluate  : 1.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 HIS
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  126 TYR
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  161 ASP
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  232 ILE
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  389 MET
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  407 ASP
Chi-restraints excluded: chain A residue  524 MET
Chi-restraints excluded: chain A residue  597 VAL
Chi-restraints excluded: chain A residue  631 ARG
Chi-restraints excluded: chain A residue  702 LEU
Chi-restraints excluded: chain A residue  725 ILE
Chi-restraints excluded: chain B residue   22 PHE
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  181 ILE
Chi-restraints excluded: chain B residue  270 LEU
Chi-restraints excluded: chain B residue  273 MET
Chi-restraints excluded: chain B residue  279 PHE
Chi-restraints excluded: chain B residue  299 VAL
Chi-restraints excluded: chain B residue  641 SER
Chi-restraints excluded: chain B residue  685 ASP
Chi-restraints excluded: chain B residue  717 LEU
Chi-restraints excluded: chain B residue  759 VAL
Chi-restraints excluded: chain B residue  787 SER
Chi-restraints excluded: chain B residue  806 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 109 optimal weight:    7.9990
   chunk 83 optimal weight:   20.0000
   chunk 35 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 121 optimal weight:    0.8980
   chunk 99 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 118 optimal weight:    2.9990
   chunk 124 optimal weight:    0.0040
   chunk 133 optimal weight:    3.9990
   chunk 31 optimal weight:    4.9990
   overall best weight:    1.5798

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

Flipped N/Q/H residues before XYZ refinement:
** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 245 HIS
** B 653 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 = 0.3784 r_free = 0.3784 target = 0.066607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.047902 restraints weight = 67073.450|
|-----------------------------------------------------------------------------|
r_work (start): 0.3225 rms_B_bonded: 5.51
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.3612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.545  12831  Z= 0.212
  Angle     :  0.691  10.614  17412  Z= 0.342
  Chirality :  0.044   0.211   1927
  Planarity :  0.005   0.063   2265
  Dihedral  :  6.217  77.460   1710
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 13.21
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.88 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 23.66 %
    Favored  : 72.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    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:  0.08 (0.22), residues: 1565
  helix:  1.00 (0.20), residues: 706
  sheet: -0.25 (0.29), residues: 310
  loop : -0.89 (0.28), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 312 
 HIS   0.006   0.001   HIS A 521 
 PHE   0.029   0.002   PHE A 602 
 TYR   0.022   0.001   TYR B 581 
 ARG   0.007   0.000   ARG A 164 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03342 (  671)
  hydrogen bonds       : angle       4.78953 ( 1971)
  covalent geometry    : bond        0.00486 (12830)
  covalent geometry    : angle       0.69125 (17412)
  Misc. bond           : bond        0.54525 (    1)

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

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

  3130 Ramachandran restraints generated.
    1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3130 Ramachandran restraints generated.
    1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 93
  time to evaluate  : 1.735 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 MET cc_start: 0.7174 (tpp) cc_final: 0.6622 (tpp)
REVERT: A   99 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8232 (mm)
REVERT: A  159 VAL cc_start: 0.7787 (OUTLIER) cc_final: 0.7549 (t)
REVERT: A  161 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.8014 (p0)
REVERT: A  176 MET cc_start: 0.7981 (tpp) cc_final: 0.7506 (tpp)
REVERT: A  480 ASP cc_start: 0.9056 (m-30) cc_final: 0.8818 (m-30)
REVERT: A  702 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8664 (mm)
REVERT: B   95 MET cc_start: 0.6667 (mpp) cc_final: 0.5206 (mpp)
REVERT: B  273 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8135 (pmm)
REVERT: B  491 MET cc_start: 0.9423 (tpp) cc_final: 0.8486 (tpp)
REVERT: B  542 MET cc_start: 0.8505 (ppp) cc_final: 0.6972 (ppp)
REVERT: B  680 MET cc_start: 0.9166 (ttp) cc_final: 0.8439 (ptm)
REVERT: B  772 MET cc_start: 0.8433 (ppp) cc_final: 0.8120 (ppp)
REVERT: B  806 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7884 (tppt)
  outliers start: 53
  outliers final: 35
  residues processed: 134
  average time/residue: 0.2876
  time to fit residues: 57.6826
Evaluate side-chains
  126 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 85
  time to evaluate  : 1.513 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 HIS
Chi-restraints excluded: chain A residue   83 HIS
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  126 TYR
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  161 ASP
Chi-restraints excluded: chain A residue  163 GLU
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  180 CYS
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  232 ILE
Chi-restraints excluded: chain A residue  286 ILE
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  407 ASP
Chi-restraints excluded: chain A residue  524 MET
Chi-restraints excluded: chain A residue  603 ILE
Chi-restraints excluded: chain A residue  631 ARG
Chi-restraints excluded: chain A residue  678 GLU
Chi-restraints excluded: chain A residue  702 LEU
Chi-restraints excluded: chain A residue  725 ILE
Chi-restraints excluded: chain A residue  780 VAL
Chi-restraints excluded: chain B residue   22 PHE
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  181 ILE
Chi-restraints excluded: chain B residue  245 HIS
Chi-restraints excluded: chain B residue  270 LEU
Chi-restraints excluded: chain B residue  273 MET
Chi-restraints excluded: chain B residue  299 VAL
Chi-restraints excluded: chain B residue  456 CYS
Chi-restraints excluded: chain B residue  597 VAL
Chi-restraints excluded: chain B residue  640 LEU
Chi-restraints excluded: chain B residue  641 SER
Chi-restraints excluded: chain B residue  685 ASP
Chi-restraints excluded: chain B residue  704 VAL
Chi-restraints excluded: chain B residue  717 LEU
Chi-restraints excluded: chain B residue  759 VAL
Chi-restraints excluded: chain B residue  787 SER
Chi-restraints excluded: chain B residue  806 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 136 optimal weight:    4.9990
   chunk 22 optimal weight:    4.9990
   chunk 150 optimal weight:    2.9990
   chunk 101 optimal weight:    0.5980
   chunk 84 optimal weight:    0.8980
   chunk 19 optimal weight:    0.4980
   chunk 68 optimal weight:    2.9990
   chunk 64 optimal weight:    0.1980
   chunk 56 optimal weight:    0.9990
   chunk 104 optimal weight:    0.5980
   chunk 3 optimal weight:    5.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 142 GLN
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 365 HIS
** B 653 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 = 0.3830 r_free = 0.3830 target = 0.067608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.049268 restraints weight = 67296.956|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 5.39
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.3792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.353  12831  Z= 0.129
  Angle     :  0.696  13.487  17412  Z= 0.332
  Chirality :  0.044   0.190   1927
  Planarity :  0.004   0.065   2265
  Dihedral  :  6.144  76.061   1710
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 13.01
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.92 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 24.17 %
    Favored  : 72.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    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:  0.31 (0.22), residues: 1565
  helix:  1.20 (0.20), residues: 706
  sheet: -0.09 (0.29), residues: 305
  loop : -0.83 (0.28), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 312 
 HIS   0.014   0.001   HIS B 245 
 PHE   0.024   0.002   PHE A 602 
 TYR   0.016   0.001   TYR B 581 
 ARG   0.004   0.000   ARG B 334 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03126 (  671)
  hydrogen bonds       : angle       4.64188 ( 1971)
  covalent geometry    : bond        0.00299 (12830)
  covalent geometry    : angle       0.69646 (17412)
  Misc. bond           : bond        0.35264 (    1)

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

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

  3130 Ramachandran restraints generated.
    1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3130 Ramachandran restraints generated.
    1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 89
  time to evaluate  : 1.448 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 MET cc_start: 0.6988 (tpp) cc_final: 0.6473 (tpp)
REVERT: A   99 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8195 (mm)
REVERT: A  159 VAL cc_start: 0.7700 (OUTLIER) cc_final: 0.7472 (t)
REVERT: A  161 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.8021 (p0)
REVERT: A  176 MET cc_start: 0.7802 (tpp) cc_final: 0.7348 (tpp)
REVERT: A  480 ASP cc_start: 0.9050 (m-30) cc_final: 0.8754 (m-30)
REVERT: A  702 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8603 (mm)
REVERT: B   43 MET cc_start: 0.8097 (mpp) cc_final: 0.7876 (mpp)
REVERT: B   95 MET cc_start: 0.6939 (mpp) cc_final: 0.5768 (mpp)
REVERT: B  273 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8011 (pmm)
REVERT: B  542 MET cc_start: 0.8251 (ppp) cc_final: 0.7716 (ppp)
REVERT: B  640 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8272 (tp)
REVERT: B  680 MET cc_start: 0.9082 (ttp) cc_final: 0.8359 (ptm)
REVERT: B  717 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8782 (tt)
REVERT: B  772 MET cc_start: 0.8368 (ppp) cc_final: 0.8052 (ppp)
REVERT: B  806 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7939 (mmmt)
  outliers start: 48
  outliers final: 36
  residues processed: 126
  average time/residue: 0.2257
  time to fit residues: 43.8025
Evaluate side-chains
  130 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 86
  time to evaluate  : 1.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 HIS
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  126 TYR
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  161 ASP
Chi-restraints excluded: chain A residue  163 GLU
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  180 CYS
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain A residue  232 ILE
Chi-restraints excluded: chain A residue  286 ILE
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  407 ASP
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  524 MET
Chi-restraints excluded: chain A residue  597 VAL
Chi-restraints excluded: chain A residue  631 ARG
Chi-restraints excluded: chain A residue  644 LEU
Chi-restraints excluded: chain A residue  698 MET
Chi-restraints excluded: chain A residue  702 LEU
Chi-restraints excluded: chain A residue  725 ILE
Chi-restraints excluded: chain A residue  780 VAL
Chi-restraints excluded: chain B residue   22 PHE
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  181 ILE
Chi-restraints excluded: chain B residue  270 LEU
Chi-restraints excluded: chain B residue  273 MET
Chi-restraints excluded: chain B residue  279 PHE
Chi-restraints excluded: chain B residue  299 VAL
Chi-restraints excluded: chain B residue  456 CYS
Chi-restraints excluded: chain B residue  597 VAL
Chi-restraints excluded: chain B residue  640 LEU
Chi-restraints excluded: chain B residue  641 SER
Chi-restraints excluded: chain B residue  685 ASP
Chi-restraints excluded: chain B residue  704 VAL
Chi-restraints excluded: chain B residue  717 LEU
Chi-restraints excluded: chain B residue  759 VAL
Chi-restraints excluded: chain B residue  766 THR
Chi-restraints excluded: chain B residue  787 SER
Chi-restraints excluded: chain B residue  806 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 155 optimal weight:    0.3980
   chunk 125 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9980
   chunk 86 optimal weight:    3.9990
   chunk 73 optimal weight:    0.8980
   chunk 132 optimal weight:    0.7980
   chunk 91 optimal weight:    0.7980
   chunk 25 optimal weight:    0.0370
   chunk 88 optimal weight:    8.9990
   chunk 145 optimal weight:    5.9990
   chunk 107 optimal weight:    6.9990
   overall best weight:    0.5858

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

Flipped N/Q/H residues before XYZ refinement:
** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.068182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.050016 restraints weight = 66910.357|
|-----------------------------------------------------------------------------|
r_work (start): 0.3309 rms_B_bonded: 5.34
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.3933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.260  12831  Z= 0.127
  Angle     :  0.701  12.419  17412  Z= 0.331
  Chirality :  0.043   0.163   1927
  Planarity :  0.004   0.064   2265
  Dihedral  :  6.081  76.429   1710
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 12.09
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.24 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 24.76 %
    Favored  : 72.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    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:  0.35 (0.22), residues: 1565
  helix:  1.25 (0.20), residues: 709
  sheet: -0.05 (0.29), residues: 305
  loop : -0.85 (0.28), residues: 551

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 312 
 HIS   0.004   0.001   HIS A 245 
 PHE   0.023   0.001   PHE A 602 
 TYR   0.014   0.001   TYR B 581 
 ARG   0.003   0.000   ARG A 215 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03044 (  671)
  hydrogen bonds       : angle       4.62045 ( 1971)
  covalent geometry    : bond        0.00301 (12830)
  covalent geometry    : angle       0.70119 (17412)
  Misc. bond           : bond        0.25960 (    1)

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

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

  3130 Ramachandran restraints generated.
    1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3130 Ramachandran restraints generated.
    1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 90
  time to evaluate  : 2.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 MET cc_start: 0.7001 (tpp) cc_final: 0.6306 (tpp)
REVERT: A   99 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8086 (mm)
REVERT: A  159 VAL cc_start: 0.7678 (OUTLIER) cc_final: 0.7457 (t)
REVERT: A  176 MET cc_start: 0.7781 (tpp) cc_final: 0.7540 (tpp)
REVERT: A  265 LEU cc_start: 0.8909 (tt) cc_final: 0.8674 (tp)
REVERT: A  480 ASP cc_start: 0.9029 (m-30) cc_final: 0.8719 (m-30)
REVERT: A  702 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8593 (mm)
REVERT: B   31 MET cc_start: 0.6269 (tpt) cc_final: 0.5239 (tpt)
REVERT: B   43 MET cc_start: 0.8199 (mpp) cc_final: 0.7998 (mpp)
REVERT: B   95 MET cc_start: 0.6845 (mpp) cc_final: 0.5866 (mpp)
REVERT: B  130 VAL cc_start: 0.9402 (t) cc_final: 0.9055 (m)
REVERT: B  273 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.7965 (pmm)
REVERT: B  424 ASP cc_start: 0.9372 (m-30) cc_final: 0.9103 (t0)
REVERT: B  542 MET cc_start: 0.8285 (ppp) cc_final: 0.7656 (ppp)
REVERT: B  640 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8242 (tp)
REVERT: B  680 MET cc_start: 0.9052 (ttp) cc_final: 0.8378 (ptm)
REVERT: B  717 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8795 (tt)
REVERT: B  772 MET cc_start: 0.8358 (ppp) cc_final: 0.8034 (ppp)
REVERT: B  806 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7921 (mmmt)
  outliers start: 43
  outliers final: 33
  residues processed: 124
  average time/residue: 0.2870
  time to fit residues: 54.9597
Evaluate side-chains
  129 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 89
  time to evaluate  : 1.513 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 HIS
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  126 TYR
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  180 CYS
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain A residue  232 ILE
Chi-restraints excluded: chain A residue  286 ILE
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  407 ASP
Chi-restraints excluded: chain A residue  524 MET
Chi-restraints excluded: chain A residue  597 VAL
Chi-restraints excluded: chain A residue  631 ARG
Chi-restraints excluded: chain A residue  644 LEU
Chi-restraints excluded: chain A residue  698 MET
Chi-restraints excluded: chain A residue  702 LEU
Chi-restraints excluded: chain A residue  725 ILE
Chi-restraints excluded: chain A residue  780 VAL
Chi-restraints excluded: chain B residue   22 PHE
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  181 ILE
Chi-restraints excluded: chain B residue  270 LEU
Chi-restraints excluded: chain B residue  273 MET
Chi-restraints excluded: chain B residue  279 PHE
Chi-restraints excluded: chain B residue  299 VAL
Chi-restraints excluded: chain B residue  456 CYS
Chi-restraints excluded: chain B residue  597 VAL
Chi-restraints excluded: chain B residue  640 LEU
Chi-restraints excluded: chain B residue  641 SER
Chi-restraints excluded: chain B residue  685 ASP
Chi-restraints excluded: chain B residue  704 VAL
Chi-restraints excluded: chain B residue  717 LEU
Chi-restraints excluded: chain B residue  759 VAL
Chi-restraints excluded: chain B residue  787 SER
Chi-restraints excluded: chain B residue  806 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 151 optimal weight:    2.9990
   chunk 59 optimal weight:    0.5980
   chunk 62 optimal weight:    0.0970
   chunk 29 optimal weight:    0.0010
   chunk 77 optimal weight:    3.9990
   chunk 10 optimal weight:   10.0000
   chunk 19 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 36 optimal weight:    0.5980
   chunk 61 optimal weight:    0.0370
   chunk 117 optimal weight:    2.9990
   overall best weight:    0.2662

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

Flipped N/Q/H residues before XYZ refinement:
** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.068572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.050383 restraints weight = 66711.712|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 5.41
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.4087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.231  12831  Z= 0.119
  Angle     :  0.711  12.375  17412  Z= 0.333
  Chirality :  0.044   0.166   1927
  Planarity :  0.004   0.065   2265
  Dihedral  :  6.000  76.443   1710
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 11.77
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.05 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 25.20 %
    Favored  : 72.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    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:  0.47 (0.22), residues: 1565
  helix:  1.38 (0.20), residues: 700
  sheet:  0.08 (0.30), residues: 306
  loop : -0.87 (0.28), residues: 559

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 312 
 HIS   0.005   0.001   HIS A 165 
 PHE   0.022   0.001   PHE B 602 
 TYR   0.010   0.001   TYR A 415 
 ARG   0.004   0.000   ARG A 215 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02965 (  671)
  hydrogen bonds       : angle       4.55392 ( 1971)
  covalent geometry    : bond        0.00277 (12830)
  covalent geometry    : angle       0.71110 (17412)
  Misc. bond           : bond        0.23124 (    1)

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

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

  3130 Ramachandran restraints generated.
    1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3130 Ramachandran restraints generated.
    1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 93
  time to evaluate  : 2.151 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 MET cc_start: 0.7075 (tpp) cc_final: 0.6413 (tpp)
REVERT: A   99 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8105 (mm)
REVERT: A  176 MET cc_start: 0.7723 (tpp) cc_final: 0.7482 (tpp)
REVERT: A  480 ASP cc_start: 0.9001 (m-30) cc_final: 0.8719 (m-30)
REVERT: A  702 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8637 (mm)
REVERT: B   31 MET cc_start: 0.6452 (tpt) cc_final: 0.5325 (tpt)
REVERT: B   95 MET cc_start: 0.6934 (mpp) cc_final: 0.5635 (mpp)
REVERT: B  130 VAL cc_start: 0.9442 (t) cc_final: 0.9088 (m)
REVERT: B  273 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.7892 (pmm)
REVERT: B  424 ASP cc_start: 0.9311 (m-30) cc_final: 0.9023 (t0)
REVERT: B  542 MET cc_start: 0.8260 (ppp) cc_final: 0.7955 (ppp)
REVERT: B  640 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8206 (tp)
REVERT: B  680 MET cc_start: 0.9021 (ttp) cc_final: 0.8401 (ptm)
REVERT: B  772 MET cc_start: 0.8327 (ppp) cc_final: 0.8007 (ppp)
REVERT: B  806 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7938 (mmmt)
  outliers start: 36
  outliers final: 25
  residues processed: 122
  average time/residue: 0.3032
  time to fit residues: 58.5139
Evaluate side-chains
  121 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 91
  time to evaluate  : 1.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 HIS
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  126 TYR
Chi-restraints excluded: chain A residue  163 GLU
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain A residue  232 ILE
Chi-restraints excluded: chain A residue  407 ASP
Chi-restraints excluded: chain A residue  597 VAL
Chi-restraints excluded: chain A residue  631 ARG
Chi-restraints excluded: chain A residue  702 LEU
Chi-restraints excluded: chain A residue  725 ILE
Chi-restraints excluded: chain A residue  780 VAL
Chi-restraints excluded: chain B residue   22 PHE
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  181 ILE
Chi-restraints excluded: chain B residue  270 LEU
Chi-restraints excluded: chain B residue  273 MET
Chi-restraints excluded: chain B residue  279 PHE
Chi-restraints excluded: chain B residue  299 VAL
Chi-restraints excluded: chain B residue  597 VAL
Chi-restraints excluded: chain B residue  640 LEU
Chi-restraints excluded: chain B residue  641 SER
Chi-restraints excluded: chain B residue  685 ASP
Chi-restraints excluded: chain B residue  704 VAL
Chi-restraints excluded: chain B residue  759 VAL
Chi-restraints excluded: chain B residue  787 SER
Chi-restraints excluded: chain B residue  806 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 104 optimal weight:    0.7980
   chunk 30 optimal weight:   10.0000
   chunk 36 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   chunk 96 optimal weight:    0.0170
   chunk 35 optimal weight:    0.9980
   chunk 37 optimal weight:    0.6980
   chunk 121 optimal weight:    1.9990
   chunk 149 optimal weight:    4.9990
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.5818

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

Flipped N/Q/H residues before XYZ refinement:
** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.068168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.049835 restraints weight = 68432.789|
|-----------------------------------------------------------------------------|
r_work (start): 0.3313 rms_B_bonded: 5.50
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.4166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.207  12831  Z= 0.128
  Angle     :  0.722  14.645  17412  Z= 0.339
  Chirality :  0.043   0.158   1927
  Planarity :  0.004   0.062   2265
  Dihedral  :  6.023  77.608   1710
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.92 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 25.20 %
    Favored  : 72.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    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:  0.46 (0.22), residues: 1565
  helix:  1.36 (0.20), residues: 702
  sheet:  0.10 (0.30), residues: 306
  loop : -0.88 (0.28), residues: 557

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 312 
 HIS   0.004   0.001   HIS A 245 
 PHE   0.028   0.002   PHE B 445 
 TYR   0.015   0.001   TYR B 581 
 ARG   0.004   0.000   ARG B 716 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03000 (  671)
  hydrogen bonds       : angle       4.55936 ( 1971)
  covalent geometry    : bond        0.00303 (12830)
  covalent geometry    : angle       0.72234 (17412)
  Misc. bond           : bond        0.20657 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6284.49 seconds
wall clock time: 112 minutes 51.13 seconds (6771.13 seconds total)