Starting phenix.real_space_refine
on Thu Aug  6 01:07:38 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ce0_45489/08_2026/9ce0_45489_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ce0_45489/08_2026/9ce0_45489.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.97
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ce0_45489/08_2026/9ce0_45489.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ce0_45489/08_2026/9ce0_45489.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ce0_45489/08_2026/9ce0_45489_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ce0_45489/08_2026/9ce0_45489_neut.cif"
  }
  resolution = 3.97
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.018
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    7957      2.51       5
     N    2188      2.21       5
     O    2338      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 120 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 12551
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6257
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 787, 6257
          Classifications: {'peptide': 787}
          Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 33, 'TRANS': 750}
    Chain: "B"
      Number of atoms: 6204
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 781, 6204
          Classifications: {'peptide': 781}
          Link IDs: {'PTRANS': 35, 'TRANS': 745}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 45
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 45
          Unusual residues: {'HEM': 1, 'OXY': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 45
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 45
          Unusual residues: {'HEM': 1, 'OXY': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.82, per 1000 atoms: 0.22
  Number of scatterers: 12551
  At special positions: 0
  Unit cell: (93.6383, 103.325, 195.349, 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    2338      8.00
     N    2188      7.00
     C    7957      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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.96
  Conformation dependent library (CDL) restraints added in 434.7 milliseconds
  

  3124 Ramachandran restraints generated.
    1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2956

  Finding SS restraints...
    Secondary structure from input PDB file:
      64 helices and 13 sheets defined
      51.0% alpha, 19.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 28
      removed outlier: 3.802A  pdb=" N   ALA A  25 " --> pdb=" O   ILE A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 52
    Processing helix  chain 'A' and resid 56 through 61
      removed outlier: 3.810A  pdb=" N   VAL A  60 " --> pdb=" O   LYS A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 68
      removed outlier: 3.929A  pdb=" N   MET A  67 " --> pdb=" O   ASN A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 87
      removed outlier: 3.647A  pdb=" N   TYR A  80 " --> pdb=" O   ALA A  76 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   GLY A  87 " --> pdb=" O   HIS A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 92
    Processing helix  chain 'A' and resid 119 through 123
    Processing helix  chain 'A' and resid 133 through 152
    Processing helix  chain 'A' and resid 170 through 178
    Processing helix  chain 'A' and resid 180 through 185
    Processing helix  chain 'A' and resid 188 through 193
    Processing helix  chain 'A' and resid 200 through 212
      removed outlier: 4.202A  pdb=" N   ILE A 204 " --> pdb=" O   ALA A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 275
    Processing helix  chain 'A' and resid 278 through 294
    Processing helix  chain 'A' and resid 352 through 383
    Processing helix  chain 'A' and resid 394 through 409
    Processing helix  chain 'A' and resid 421 through 429
    Processing helix  chain 'A' and resid 430 through 449
      removed outlier: 4.219A  pdb=" N   GLN A 436 " --> pdb=" O   ALA A 432 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   GLU A 440 " --> pdb=" O   GLN A 436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 471 through 485
    Processing helix  chain 'A' and resid 512 through 531
    Processing helix  chain 'A' and resid 542 through 563
      removed outlier: 3.627A  pdb=" N   ARG A 549 " --> pdb=" O   MET A 545 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 609
      Proline residue:  A 604  - end of helix
    Processing helix  chain 'A' and resid 611 through 634
    Processing helix  chain 'A' and resid 645 through 648
    Processing helix  chain 'A' and resid 650 through 652
      No H-bonds generated for 'chain 'A' and resid 650 through 652'
    Processing helix  chain 'A' and resid 653 through 665
      removed outlier: 4.265A  pdb=" N   ALA A 661 " --> pdb=" O   GLN A 657 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 688 through 699
    Processing helix  chain 'A' and resid 710 through 720
      removed outlier: 3.758A  pdb=" N   LEU A 720 " --> pdb=" O   ARG A 716 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 728 through 736
      removed outlier: 3.813A  pdb=" N   ARG A 734 " --> pdb=" O   SER A 730 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   LEU A 736 " --> pdb=" O   VAL A 732 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 738 through 756
      removed outlier: 3.615A  pdb=" N   LEU A 742 " --> pdb=" O   GLU A 738 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 766 through 777
    Processing helix  chain 'A' and resid 794 through 803
      removed outlier: 3.859A  pdb=" N   SER A 800 " --> pdb=" O   PRO A 796 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 23 through 28
    Processing helix  chain 'B' and resid 46 through 54
    Processing helix  chain 'B' and resid 56 through 61
    Processing helix  chain 'B' and resid 64 through 68
    Processing helix  chain 'B' and resid 73 through 75
      No H-bonds generated for 'chain 'B' and resid 73 through 75'
    Processing helix  chain 'B' and resid 76 through 88
      removed outlier: 3.621A  pdb=" N   GLY B  88 " --> pdb=" O   ASN B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 89 through 92
    Processing helix  chain 'B' and resid 134 through 153
    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 201 through 210
      removed outlier: 4.054A  pdb=" N   ARG B 205 " --> pdb=" O   ASP B 201 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 256 through 276
    Processing helix  chain 'B' and resid 278 through 294
    Processing helix  chain 'B' and resid 352 through 377
    Processing helix  chain 'B' and resid 394 through 408
      removed outlier: 3.686A  pdb=" N   LYS B 408 " --> pdb=" O   ASP B 404 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 421 through 447
      removed outlier: 4.142A  pdb=" N   VAL B 425 " --> pdb=" O   HIS B 421 " (cutoff:3.500A)
      removed outlier: 8.024A  pdb=" N   TYR B 431 " --> pdb=" O   ASP B 427 " (cutoff:3.500A)
      removed outlier: 9.336A  pdb=" N   ALA B 432 " --> pdb=" O   SER B 428 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   TRP B 433 " --> pdb=" O   LEU B 429 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   GLN B 436 " --> pdb=" O   ALA B 432 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   GLU B 447 " --> pdb=" O   ASN B 443 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 471 through 486
      removed outlier: 3.755A  pdb=" N   VAL B 486 " --> pdb=" O   LEU B 482 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 512 through 531
    Processing helix  chain 'B' and resid 539 through 562
    Processing helix  chain 'B' and resid 598 through 610
      Proline residue:  B 604  - end of helix
    Processing helix  chain 'B' and resid 611 through 632
    Processing helix  chain 'B' and resid 643 through 648
    Processing helix  chain 'B' and resid 650 through 654
      removed outlier: 3.921A  pdb=" N   GLN B 653 " --> pdb=" O   ARG B 650 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   LEU B 654 " --> pdb=" O   SER B 651 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 650 through 654'
    Processing helix  chain 'B' and resid 655 through 665
      removed outlier: 4.914A  pdb=" N   ALA B 661 " --> pdb=" O   GLN B 657 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 677 through 683
    Processing helix  chain 'B' and resid 686 through 699
      removed outlier: 3.706A  pdb=" N   LYS B 690 " --> pdb=" O   THR B 686 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 709 through 720
    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
    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: 3.764A  pdb=" N   GLN A 168 " --> pdb=" O   VAL A 159 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 308 through 314
      removed outlier: 6.615A  pdb=" N   LEU A 301 " --> pdb=" O   TRP A 312 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   SER A 314 " --> pdb=" O   VAL A 299 " (cutoff:3.500A)
      removed outlier: 7.203A  pdb=" N   VAL A 299 " --> pdb=" O   SER A 314 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   GLN A 343 " --> pdb=" O   SER A 300 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   ALA A 339 " --> pdb=" O   LEU A 304 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   ILE A 331 " --> pdb=" O   ALA A 339 " (cutoff:3.500A)
      removed outlier: 4.944A  pdb=" N   ILE A 341 " --> pdb=" O   ALA A 329 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   ALA A 329 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   GLN A 343 " --> pdb=" O   TRP A 327 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   TRP A 327 " --> pdb=" O   GLN A 343 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   LYS A 345 " --> pdb=" O   GLN A 325 " (cutoff:3.500A)
      removed outlier: 6.108A  pdb=" N   GLN A 325 " --> pdb=" O   LYS A 345 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 454 through 459
      removed outlier: 5.507A  pdb=" N   LEU A 455 " --> pdb=" O   VAL A 466 " (cutoff:3.500A)
      removed outlier: 7.081A  pdb=" N   VAL A 466 " --> pdb=" O   LEU A 455 " (cutoff:3.500A)
      removed outlier: 5.296A  pdb=" N   ARG A 457 " --> pdb=" O   VAL A 464 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   VAL A 464 " --> pdb=" O   ARG A 457 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   GLU A 459 " --> pdb=" O   GLN A 462 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 490 through 492
    Processing sheet with id=AA6, first strand: chain 'A' and resid 566 through 573
      removed outlier: 4.453A  pdb=" N   TRP A 589 " --> pdb=" O   VAL A 597 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 566 through 573
      removed outlier: 4.652A  pdb=" N   ASN A 643 " --> pdb=" O   ALA A 585 " (cutoff:3.500A)
      removed outlier: 7.597A  pdb=" N   ALA A 587 " --> pdb=" O   ASN A 643 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   GLU A 675 " --> pdb=" O   VAL A 642 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   GLY A 701 " --> pdb=" O   LEU A 672 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   LEU A 702 " --> pdb=" O   GLU A 724 " (cutoff:3.500A)
      removed outlier: 7.696A  pdb=" N   LYS A 726 " --> pdb=" O   LEU A 702 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   VAL A 704 " --> pdb=" O   LYS A 726 " (cutoff:3.500A)
      removed outlier: 6.154A  pdb=" N   ILE A 725 " --> pdb=" O   VAL A 760 " (cutoff:3.500A)
      removed outlier: 7.659A  pdb=" N   GLU A 762 " --> pdb=" O   ILE A 725 " (cutoff:3.500A)
      removed outlier: 7.075A  pdb=" N   ILE A 727 " --> pdb=" O   GLU A 762 " (cutoff:3.500A)
      removed outlier: 7.806A  pdb=" N   VAL A 764 " --> pdb=" O   ILE A 727 " (cutoff:3.500A)
      removed outlier: 7.837A  pdb=" N   GLN A 782 " --> pdb=" O   VAL A 759 " (cutoff:3.500A)
      removed outlier: 6.002A  pdb=" N   ALA A 761 " --> pdb=" O   GLN A 782 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 42 through 45
      removed outlier: 6.673A  pdb=" N   LEU B  35 " --> pdb=" O   MET B  43 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   PHE B  45 " --> pdb=" O   ALA B  33 " (cutoff:3.500A)
      removed outlier: 7.310A  pdb=" N   ALA B  33 " --> pdb=" O   PHE B  45 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   GLY B  32 " --> pdb=" O   VAL B 130 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 166 through 168
      removed outlier: 6.055A  pdb=" N   VAL B 159 " --> pdb=" O   VAL B 167 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 308 through 314
      removed outlier: 6.714A  pdb=" N   LEU B 301 " --> pdb=" O   TRP B 312 " (cutoff:3.500A)
      removed outlier: 4.651A  pdb=" N   SER B 314 " --> pdb=" O   VAL B 299 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   VAL B 299 " --> pdb=" O   SER B 314 " (cutoff:3.500A)
      removed outlier: 7.083A  pdb=" N   ALA B 339 " --> pdb=" O   LEU B 304 " (cutoff:3.500A)
      removed outlier: 6.145A  pdb=" N   ILE B 331 " --> pdb=" O   ALA B 339 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   ILE B 341 " --> pdb=" O   ALA B 329 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   ALA B 329 " --> pdb=" O   ILE B 341 " (cutoff:3.500A)
      removed outlier: 4.514A  pdb=" N   GLN B 343 " --> pdb=" O   TRP B 327 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   TRP B 327 " --> pdb=" O   GLN B 343 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   LYS B 345 " --> pdb=" O   GLN B 325 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   GLN B 325 " --> pdb=" O   LYS B 345 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 454 through 459
      removed outlier: 7.109A  pdb=" N   GLN B 462 " --> pdb=" O   ILE B 458 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 672 through 674
      removed outlier: 6.344A  pdb=" N   LEU B 640 " --> pdb=" O   THR B 673 " (cutoff:3.500A)
      removed outlier: 8.264A  pdb=" N   SER B 641 " --> pdb=" O   TYR B 581 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   ILE B 583 " --> pdb=" O   SER B 641 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   GLN B 572 " --> pdb=" O   TYR B 581 " (cutoff:3.500A)
      removed outlier: 4.538A  pdb=" N   ILE B 583 " --> pdb=" O   GLN B 570 " (cutoff:3.500A)
      removed outlier: 5.809A  pdb=" N   GLN B 570 " --> pdb=" O   ILE B 583 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   ALA B 585 " --> pdb=" O   VAL B 568 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   VAL B 568 " --> pdb=" O   ALA B 585 " (cutoff:3.500A)
      removed outlier: 5.067A  pdb=" N   ALA B 587 " --> pdb=" O   LYS B 566 " (cutoff:3.500A)
      removed outlier: 7.072A  pdb=" N   LYS B 566 " --> pdb=" O   ALA B 587 " (cutoff:3.500A)
      removed outlier: 6.267A  pdb=" N   VAL B 759 " --> pdb=" O   VAL B 780 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   ILE B 725 " --> pdb=" O   VAL B 760 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 590 through 591

    696 hydrogen bonds defined for protein.
    1998 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.49

  Time building geometry restraints manager: 1.25 seconds

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

  Histogram of bond lengths:
        1.21 -     1.38: 4943
        1.38 -     1.56: 7750
        1.56 -     1.73: 0
        1.73 -     1.91: 116
        1.91 -     2.08: 8
  Bond restraints: 12817
  Sorted by residual:
  bond pdb=" O1  OXY B 902 "
       pdb=" O2  OXY B 902 "
    ideal  model  delta    sigma   weight residual
    1.109  1.206 -0.097 2.00e-02 2.50e+03 2.37e+01
  bond pdb=" O1  OXY A 902 "
       pdb=" O2  OXY A 902 "
    ideal  model  delta    sigma   weight residual
    1.109  1.206 -0.097 2.00e-02 2.50e+03 2.37e+01
  bond pdb=" CA  SER A 600 "
       pdb=" C   SER A 600 "
    ideal  model  delta    sigma   weight residual
    1.522  1.475  0.047 1.45e-02 4.76e+03 1.03e+01
  bond pdb=" N   PHE B 386 "
       pdb=" CA  PHE B 386 "
    ideal  model  delta    sigma   weight residual
    1.456  1.484 -0.028 1.13e-02 7.83e+03 6.19e+00
  bond pdb=" N   ILE B 384 "
       pdb=" CA  ILE B 384 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.036 1.90e-02 2.77e+03 3.60e+00
  ... (remaining 12812 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.45: 16472
        1.45 -     2.90: 803
        2.90 -     4.36: 102
        4.36 -     5.81: 8
        5.81 -     7.26: 3
  Bond angle restraints: 17388
  Sorted by residual:
  angle pdb=" N   ILE A 148 "
        pdb=" CA  ILE A 148 "
        pdb=" C   ILE A 148 "
      ideal   model   delta    sigma   weight residual
     110.72  106.18    4.54 1.01e+00 9.80e-01 2.02e+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  109.61    4.56 1.14e+00 7.69e-01 1.60e+01
  angle pdb=" C   GLU B 793 "
        pdb=" N   GLU B 794 "
        pdb=" CA  GLU B 794 "
      ideal   model   delta    sigma   weight residual
     121.54  128.65   -7.11 1.91e+00 2.74e-01 1.39e+01
  angle pdb=" N   GLN B 385 "
        pdb=" CA  GLN B 385 "
        pdb=" C   GLN B 385 "
      ideal   model   delta    sigma   weight residual
     113.40  108.14    5.26 1.47e+00 4.63e-01 1.28e+01
  angle pdb=" N   ASP A 151 "
        pdb=" CA  ASP A 151 "
        pdb=" C   ASP A 151 "
      ideal   model   delta    sigma   weight residual
     111.28  107.61    3.67 1.09e+00 8.42e-01 1.13e+01
  ... (remaining 17383 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.75: 6911
       17.75 -    35.50: 648
       35.50 -    53.25: 127
       53.25 -    71.00: 41
       71.00 -    88.75: 17
  Dihedral angle restraints: 7744
    sinusoidal: 3191
      harmonic: 4553
  Sorted by residual:
  dihedral pdb=" CA  GLN B 657 "
           pdb=" C   GLN B 657 "
           pdb=" N   VAL B 658 "
           pdb=" CA  VAL B 658 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.15   28.85     0      5.00e+00 4.00e-02 3.33e+01
  dihedral pdb=" CA  GLY A 227 "
           pdb=" C   GLY A 227 "
           pdb=" N   GLU A 228 "
           pdb=" CA  GLU A 228 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.83  -28.17     0      5.00e+00 4.00e-02 3.17e+01
  dihedral pdb=" CA  LEU A 720 "
           pdb=" C   LEU A 720 "
           pdb=" N   PRO A 721 "
           pdb=" CA  PRO A 721 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.42  -25.58     0      5.00e+00 4.00e-02 2.62e+01
  ... (remaining 7741 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 1405
       0.040 -    0.080: 363
       0.080 -    0.120: 137
       0.120 -    0.160: 16
       0.160 -    0.200: 1
  Chirality restraints: 1922
  Sorted by residual:
  chirality pdb=" CA  ILE B 384 "
            pdb=" N   ILE B 384 "
            pdb=" C   ILE B 384 "
            pdb=" CB  ILE B 384 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 1.00e+00
  chirality pdb=" CA  ILE A 331 "
            pdb=" N   ILE A 331 "
            pdb=" C   ILE A 331 "
            pdb=" CB  ILE A 331 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.15e-01
  chirality pdb=" CA  ILE A  69 "
            pdb=" N   ILE A  69 "
            pdb=" C   ILE A  69 "
            pdb=" CB  ILE A  69 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.58e-01
  ... (remaining 1919 not shown)

  Planarity restraints: 2261
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 155 "   -0.037 5.00e-02 4.00e+02   5.58e-02 4.98e+00
        pdb=" N   PRO A 156 "    0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO A 156 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 156 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 266 "    0.011 2.00e-02 2.50e+03   2.22e-02 4.93e+00
        pdb=" C   GLU B 266 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   GLU B 266 "    0.014 2.00e-02 2.50e+03
        pdb=" N   GLY B 267 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 144 "   -0.011 2.00e-02 2.50e+03   2.14e-02 4.57e+00
        pdb=" C   ARG B 144 "    0.037 2.00e-02 2.50e+03
        pdb=" O   ARG B 144 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   GLN B 145 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 2258 not shown)

  Histogram of nonbonded interaction distances:
        1.93 -     2.52: 184
        2.52 -     3.12: 10812
        3.12 -     3.71: 20858
        3.71 -     4.31: 27856
        4.31 -     4.90: 45103
  Nonbonded interactions: 104813
  Sorted by model distance:
  nonbonded pdb=" O   LYS A 140 "
            pdb=" OG1 THR A 143 "
     model   vdw
     1.931 3.040
  nonbonded pdb=" O   ALA A 272 "
            pdb=" OG  SER A 275 "
     model   vdw
     1.963 3.040
  nonbonded pdb=" O   ASN A  84 "
            pdb=" OH  TYR A 126 "
     model   vdw
     1.979 3.040
  nonbonded pdb=" OG  SER B 632 "
            pdb=" OE1 GLN B 633 "
     model   vdw
     1.997 3.040
  nonbonded pdb=" O   GLY B 708 "
            pdb=" OG1 THR B 709 "
     model   vdw
     2.048 3.040
  ... (remaining 104808 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 377 or resid 384 through 902))
  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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.220
  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:             0.000
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     11.410
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7008
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.714  12819  Z= 0.240
  Angle     :  0.693   7.261  17388  Z= 0.460
  Chirality :  0.042   0.200   1922
  Planarity :  0.006   0.069   2261
  Dihedral  : 15.095  88.749   4788
  Min Nonbonded Distance : 1.931

Molprobity Statistics.
  All-atom Clashscore : 16.34
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.27 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  9.12 %
    Favored  : 90.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.00 (0.21), residues: 1562
  helix:  0.30 (0.20), residues: 713
  sheet: -0.96 (0.29), residues: 322
  loop : -1.66 (0.27), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 164 
 TYR   0.018   0.001   TYR B 454 
 PHE   0.022   0.002   PHE A 602 
 TRP   0.013   0.001   TRP A 665 
 HIS   0.005   0.001   HIS A 365 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00430 /  0.24 (12817)
  covalent geometry    : angle       0.69275 /  0.46 (17388)
  hydrogen bonds       : bond        0.10649 /  6.92 (  688)
  hydrogen bonds       : angle       6.47419 /  4.59 ( 1998)
  Misc. bond           : bond        0.70627 / 41.71 (    2)

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

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

  3124 Ramachandran restraints generated.
    1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3124 Ramachandran restraints generated.
    1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 138
  time to evaluate  : 0.447 
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: A   30 MET cc_start: -0.0135 (ptm) cc_final: -0.0388 (ptt)
REVERT: A   43 MET cc_start: 0.2565 (mpp) cc_final: 0.2218 (mpp)
REVERT: B  416 LEU cc_start: 0.9075 (tp) cc_final: 0.8350 (tp)
  outliers start: 2
  outliers final: 0
  residues processed: 140
  average time/residue: 0.1125
  time to fit residues: 22.3141
Evaluate side-chains
  87 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 98 optimal weight:    6.9990
   chunk 107 optimal weight:   10.0000
   chunk 10 optimal weight:   30.0000
   chunk 66 optimal weight:    0.7980
   chunk 130 optimal weight:    0.7980
   chunk 124 optimal weight:    0.3980
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:    0.8980
   chunk 122 optimal weight:    0.7980
   chunk 91 optimal weight:    4.9990
   chunk 149 optimal weight:    7.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 343 GLN
** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 670 HIS
B 139 GLN
B 217 GLN
B 248 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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.070088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.046494 restraints weight = 93172.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.046145 restraints weight = 72323.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.046661 restraints weight = 56909.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.046907 restraints weight = 49678.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.047121 restraints weight = 44334.425|
|-----------------------------------------------------------------------------|
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.1968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.247  12819  Z= 0.168
  Angle     :  0.743   9.181  17388  Z= 0.376
  Chirality :  0.047   0.181   1922
  Planarity :  0.006   0.054   2261
  Dihedral  :  6.411  76.460   1707
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.74 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 13.09 %
    Favored  : 85.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.71 (0.22), residues: 1562
  helix:  0.40 (0.19), residues: 708
  sheet: -0.77 (0.28), residues: 345
  loop : -1.32 (0.29), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 112 
 TYR   0.018   0.001   TYR B 179 
 PHE   0.024   0.002   PHE B 602 
 TRP   0.013   0.001   TRP A 589 
 HIS   0.007   0.001   HIS A  77 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00349 /  0.17 (12817)
  covalent geometry    : angle       0.74270 /  0.38 (17388)
  hydrogen bonds       : bond        0.04466 /  2.99 (  688)
  hydrogen bonds       : angle       5.59137 /  3.97 ( 1998)
  Misc. bond           : bond        0.22228 / 12.96 (    2)

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

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

  3124 Ramachandran restraints generated.
    1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3124 Ramachandran restraints generated.
    1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 91
  time to evaluate  : 0.398 
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  343 GLN cc_start: 0.9418 (OUTLIER) cc_final: 0.9172 (tm-30)
REVERT: B  253 PHE cc_start: 0.8713 (m-80) cc_final: 0.8298 (m-10)
REVERT: B  772 MET cc_start: 0.9365 (mtm) cc_final: 0.9026 (ptp)
  outliers start: 21
  outliers final: 4
  residues processed: 107
  average time/residue: 0.1058
  time to fit residues: 16.5790
Evaluate side-chains
  83 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 78
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  343 GLN
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain B residue  205 ARG
Chi-restraints excluded: chain B residue  685 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 130 optimal weight:    0.9980
   chunk 101 optimal weight:    0.8980
   chunk 105 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0670
   chunk 88 optimal weight:   30.0000
   chunk 54 optimal weight:    2.9990
   chunk 126 optimal weight:    3.9990
   chunk 44 optimal weight:    4.9990
   chunk 9 optimal weight:    6.9990
   chunk 17 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 70.2828 > 50:)
   chunk 48 optimal weight:    3.9990
   overall best weight:    1.1922

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 365 HIS
A 421 HIS
** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 663 HIS
B 142 GLN
B 248 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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.069062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.045612 restraints weight = 96210.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.045068 restraints weight = 75553.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.045616 restraints weight = 59831.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.045834 restraints weight = 51830.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.046084 restraints weight = 46442.567|
|-----------------------------------------------------------------------------|
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.2390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.314  12819  Z= 0.165
  Angle     :  0.697  11.089  17388  Z= 0.350
  Chirality :  0.044   0.165   1922
  Planarity :  0.005   0.061   2261
  Dihedral  :  6.241  74.548   1707
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 11.87
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.93 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 13.68 %
    Favored  : 84.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.56 (0.22), residues: 1562
  helix:  0.51 (0.19), residues: 702
  sheet: -0.68 (0.28), residues: 338
  loop : -1.20 (0.29), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 112 
 TYR   0.013   0.001   TYR B 454 
 PHE   0.023   0.002   PHE A 602 
 TRP   0.009   0.001   TRP A 211 
 HIS   0.005   0.001   HIS A  77 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00356 /  0.16 (12817)
  covalent geometry    : angle       0.69732 /  0.35 (17388)
  hydrogen bonds       : bond        0.04039 /  2.74 (  688)
  hydrogen bonds       : angle       5.52905 /  3.90 ( 1998)
  Misc. bond           : bond        0.23631 / 14.59 (    2)

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

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

  3124 Ramachandran restraints generated.
    1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3124 Ramachandran restraints generated.
    1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 82
  time to evaluate  : 0.492 
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: A  389 MET cc_start: 0.8611 (tmm) cc_final: 0.8277 (tmm)
REVERT: A  698 MET cc_start: 0.9362 (mpp) cc_final: 0.9075 (mpp)
REVERT: B  545 MET cc_start: 0.9001 (tmm) cc_final: 0.8771 (tmm)
REVERT: B  772 MET cc_start: 0.9488 (mtm) cc_final: 0.9058 (ptp)
  outliers start: 31
  outliers final: 9
  residues processed: 107
  average time/residue: 0.1147
  time to fit residues: 18.1864
Evaluate side-chains
  86 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  615 ILE
Chi-restraints excluded: chain B residue  597 VAL
Chi-restraints excluded: chain B residue  640 LEU
Chi-restraints excluded: chain B residue  682 MET
Chi-restraints excluded: chain B residue  685 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 48 optimal weight:    7.9990
   chunk 63 optimal weight:    0.0770
   chunk 133 optimal weight:    0.4980
   chunk 51 optimal weight:    0.9990
   chunk 88 optimal weight:    9.9990
   chunk 33 optimal weight:    2.9990
   chunk 55 optimal weight:    0.8980
   chunk 132 optimal weight:    2.9990
   chunk 112 optimal weight:    5.9990
   chunk 155 optimal weight:    0.9980
   chunk 151 optimal weight:    4.9990
   overall best weight:    0.6940

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 152 HIS
B 397 ASN
B 653 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.069224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.046106 restraints weight = 94864.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.045646 restraints weight = 74210.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.046088 restraints weight = 60734.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.046675 restraints weight = 51622.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.046765 restraints weight = 43887.887|
|-----------------------------------------------------------------------------|
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.2881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.280  12819  Z= 0.134
  Angle     :  0.692  11.176  17388  Z= 0.344
  Chirality :  0.044   0.155   1922
  Planarity :  0.005   0.053   2261
  Dihedral  :  6.134  72.814   1707
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.12 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 13.90 %
    Favored  : 83.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.42 (0.22), residues: 1562
  helix:  0.61 (0.19), residues: 710
  sheet: -0.55 (0.28), residues: 336
  loop : -1.18 (0.29), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG B 358 
 TYR   0.008   0.001   TYR B 454 
 PHE   0.023   0.002   PHE A 602 
 TRP   0.009   0.001   TRP A 110 
 HIS   0.006   0.001   HIS B 365 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00292 /  0.13 (12817)
  covalent geometry    : angle       0.69229 /  0.34 (17388)
  hydrogen bonds       : bond        0.03738 /  2.54 (  688)
  hydrogen bonds       : angle       5.28794 /  3.72 ( 1998)
  Misc. bond           : bond        0.20044 / 12.49 (    2)

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

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

  3124 Ramachandran restraints generated.
    1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3124 Ramachandran restraints generated.
    1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 81
  time to evaluate  : 0.486 
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  176 MET cc_start: 0.9146 (ptm) cc_final: 0.8858 (ptt)
REVERT: A  323 ASN cc_start: 0.9507 (m110) cc_final: 0.9141 (p0)
REVERT: A  389 MET cc_start: 0.8523 (tmm) cc_final: 0.8185 (tmm)
REVERT: A  456 CYS cc_start: 0.6871 (OUTLIER) cc_final: 0.6328 (t)
REVERT: A  698 MET cc_start: 0.9226 (mpp) cc_final: 0.9002 (mpp)
REVERT: B   43 MET cc_start: 0.0581 (mtp) cc_final: 0.0343 (mpp)
REVERT: B  139 GLN cc_start: 0.9149 (OUTLIER) cc_final: 0.8698 (tm-30)
REVERT: B  177 PHE cc_start: 0.9373 (m-10) cc_final: 0.8967 (m-80)
REVERT: B  210 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9088 (pp)
REVERT: B  545 MET cc_start: 0.8995 (tmm) cc_final: 0.8761 (tmm)
REVERT: B  680 MET cc_start: 0.9153 (ttm) cc_final: 0.8547 (ptm)
REVERT: B  772 MET cc_start: 0.9521 (mtm) cc_final: 0.9041 (ptp)
  outliers start: 34
  outliers final: 16
  residues processed: 109
  average time/residue: 0.1069
  time to fit residues: 17.7036
Evaluate side-chains
  91 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 72
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  306 ASN
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  420 ASP
Chi-restraints excluded: chain A residue  456 CYS
Chi-restraints excluded: chain A residue  615 ILE
Chi-restraints excluded: chain A residue  625 ARG
Chi-restraints excluded: chain A residue  654 LEU
Chi-restraints excluded: chain B residue  139 GLN
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  414 VAL
Chi-restraints excluded: chain B residue  452 ASP
Chi-restraints excluded: chain B residue  597 VAL
Chi-restraints excluded: chain B residue  640 LEU
Chi-restraints excluded: chain B residue  685 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 56 optimal weight:    4.9990
   chunk 66 optimal weight:    6.9990
   chunk 74 optimal weight:    4.9990
   chunk 138 optimal weight:    1.9990
   chunk 60 optimal weight:    0.7980
   chunk 87 optimal weight:   10.0000
   chunk 133 optimal weight:    4.9990
   chunk 15 optimal weight:    6.9990
   chunk 99 optimal weight:    8.9990
   chunk 49 optimal weight:    5.9990
   chunk 146 optimal weight:    7.9990
   overall best weight:    3.5588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 343 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 = 0.3669 r_free = 0.3669 target = 0.065440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.042216 restraints weight = 98302.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.041711 restraints weight = 78845.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 15)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.041961 restraints weight = 63025.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.041961 restraints weight = 55025.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.041961 restraints weight = 55025.957|
|-----------------------------------------------------------------------------|
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.3409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.325  12819  Z= 0.326
  Angle     :  0.831  11.092  17388  Z= 0.419
  Chirality :  0.046   0.182   1922
  Planarity :  0.006   0.055   2261
  Dihedral  :  6.293  67.790   1707
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 20.33
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.57 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 14.63 %
    Favored  : 82.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.71 (0.21), residues: 1562
  helix:  0.34 (0.19), residues: 711
  sheet: -0.75 (0.28), residues: 337
  loop : -1.25 (0.29), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 358 
 TYR   0.019   0.002   TYR B 454 
 PHE   0.025   0.003   PHE A 602 
 TRP   0.022   0.002   TRP A 231 
 HIS   0.009   0.002   HIS A 521 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00684 /  0.33 (12817)
  covalent geometry    : angle       0.83083 /  0.42 (17388)
  hydrogen bonds       : bond        0.04361 /  3.04 (  688)
  hydrogen bonds       : angle       5.69514 /  4.02 ( 1998)
  Misc. bond           : bond        0.23400 / 14.57 (    2)

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

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

  3124 Ramachandran restraints generated.
    1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3124 Ramachandran restraints generated.
    1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 72
  time to evaluate  : 0.460 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  323 ASN cc_start: 0.9433 (m110) cc_final: 0.9097 (p0)
REVERT: A  389 MET cc_start: 0.8767 (tmm) cc_final: 0.8211 (tmm)
REVERT: A  456 CYS cc_start: 0.5776 (OUTLIER) cc_final: 0.5507 (t)
REVERT: A  758 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8793 (p)
REVERT: B   30 MET cc_start: -0.3053 (tpt) cc_final: -0.3315 (tpt)
REVERT: B  131 ARG cc_start: 0.9016 (mmp80) cc_final: 0.8774 (tmt170)
REVERT: B  253 PHE cc_start: 0.8540 (m-10) cc_final: 0.8016 (m-80)
REVERT: B  542 MET cc_start: 0.9188 (ptt) cc_final: 0.8781 (ptt)
REVERT: B  772 MET cc_start: 0.9608 (mtm) cc_final: 0.9153 (ptp)
REVERT: B  795 ILE cc_start: 0.9130 (OUTLIER) cc_final: 0.8891 (mt)
REVERT: B  799 MET cc_start: 0.9140 (ttt) cc_final: 0.8130 (ppp)
  outliers start: 41
  outliers final: 25
  residues processed: 108
  average time/residue: 0.0982
  time to fit residues: 16.8062
Evaluate side-chains
  96 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 68
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  306 ASN
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  420 ASP
Chi-restraints excluded: chain A residue  456 CYS
Chi-restraints excluded: chain A residue  472 VAL
Chi-restraints excluded: chain A residue  580 LEU
Chi-restraints excluded: chain A residue  597 VAL
Chi-restraints excluded: chain A residue  615 ILE
Chi-restraints excluded: chain A residue  625 ARG
Chi-restraints excluded: chain A residue  654 LEU
Chi-restraints excluded: chain A residue  758 THR
Chi-restraints excluded: chain B residue   31 MET
Chi-restraints excluded: chain B residue  166 ILE
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  252 THR
Chi-restraints excluded: chain B residue  414 VAL
Chi-restraints excluded: chain B residue  452 ASP
Chi-restraints excluded: chain B residue  472 VAL
Chi-restraints excluded: chain B residue  573 ILE
Chi-restraints excluded: chain B residue  640 LEU
Chi-restraints excluded: chain B residue  685 ASP
Chi-restraints excluded: chain B residue  795 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 16 optimal weight:    0.0170
   chunk 62 optimal weight:    1.9990
   chunk 119 optimal weight:    1.9990
   chunk 79 optimal weight:   20.0000
   chunk 136 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   chunk 146 optimal weight:    2.9990
   chunk 36 optimal weight:    0.6980
   chunk 154 optimal weight:    0.9990
   chunk 28 optimal weight:    5.9990
   chunk 90 optimal weight:    0.6980
   overall best weight:    0.6220

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 168 GLN
** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 343 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 = 0.3719 r_free = 0.3719 target = 0.067628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.044410 restraints weight = 95875.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.043838 restraints weight = 74793.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 14)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.044190 restraints weight = 61129.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.044628 restraints weight = 52426.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.044628 restraints weight = 47661.249|
|-----------------------------------------------------------------------------|
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.3610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.293  12819  Z= 0.140
  Angle     :  0.734  10.462  17388  Z= 0.357
  Chirality :  0.045   0.199   1922
  Planarity :  0.005   0.046   2261
  Dihedral  :  6.130  68.546   1707
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 13.90
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.87 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 16.10 %
    Favored  : 81.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.46 (0.22), residues: 1562
  helix:  0.54 (0.19), residues: 720
  sheet: -0.59 (0.28), residues: 331
  loop : -1.16 (0.29), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 358 
 TYR   0.008   0.001   TYR B 581 
 PHE   0.023   0.002   PHE A 602 
 TRP   0.009   0.001   TRP B  53 
 HIS   0.005   0.001   HIS B 152 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00312 /  0.14 (12817)
  covalent geometry    : angle       0.73395 /  0.36 (17388)
  hydrogen bonds       : bond        0.03665 /  2.54 (  688)
  hydrogen bonds       : angle       5.41460 /  3.81 ( 1998)
  Misc. bond           : bond        0.20804 / 13.00 (    2)

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

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

  3124 Ramachandran restraints generated.
    1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3124 Ramachandran restraints generated.
    1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 72
  time to evaluate  : 0.487 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  389 MET cc_start: 0.8713 (tmm) cc_final: 0.8140 (tmm)
REVERT: A  456 CYS cc_start: 0.7576 (OUTLIER) cc_final: 0.7057 (t)
REVERT: A  698 MET cc_start: 0.9413 (mpp) cc_final: 0.9126 (mpp)
REVERT: B   30 MET cc_start: -0.2454 (tpt) cc_final: -0.2768 (tpt)
REVERT: B  139 GLN cc_start: 0.9159 (OUTLIER) cc_final: 0.8725 (tm-30)
REVERT: B  542 MET cc_start: 0.9080 (ptt) cc_final: 0.7828 (ptp)
REVERT: B  545 MET cc_start: 0.9067 (tmm) cc_final: 0.8311 (ppp)
REVERT: B  772 MET cc_start: 0.9608 (mtm) cc_final: 0.9115 (ptp)
REVERT: B  799 MET cc_start: 0.9112 (ttt) cc_final: 0.8246 (ppp)
  outliers start: 30
  outliers final: 20
  residues processed: 96
  average time/residue: 0.1102
  time to fit residues: 16.1081
Evaluate side-chains
  91 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 69
  time to evaluate  : 0.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  306 ASN
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  420 ASP
Chi-restraints excluded: chain A residue  456 CYS
Chi-restraints excluded: chain A residue  597 VAL
Chi-restraints excluded: chain A residue  615 ILE
Chi-restraints excluded: chain A residue  654 LEU
Chi-restraints excluded: chain B residue   31 MET
Chi-restraints excluded: chain B residue  139 GLN
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  252 THR
Chi-restraints excluded: chain B residue  414 VAL
Chi-restraints excluded: chain B residue  452 ASP
Chi-restraints excluded: chain B residue  640 LEU
Chi-restraints excluded: chain B residue  685 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 71 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9980
   chunk 46 optimal weight:    0.0870
   chunk 69 optimal weight:    3.9990
   chunk 72 optimal weight:    0.8980
   chunk 97 optimal weight:    1.9990
   chunk 110 optimal weight:    0.6980
   chunk 8 optimal weight:    5.9990
   chunk 132 optimal weight:    0.9990
   overall best weight:    0.6958

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 343 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 = 0.3727 r_free = 0.3727 target = 0.067843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.044597 restraints weight = 97021.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.044070 restraints weight = 75092.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.044414 restraints weight = 58760.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.044414 restraints weight = 50367.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.044414 restraints weight = 50367.642|
|-----------------------------------------------------------------------------|
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.3852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.291  12819  Z= 0.134
  Angle     :  0.722   9.231  17388  Z= 0.351
  Chirality :  0.045   0.296   1922
  Planarity :  0.005   0.047   2261
  Dihedral  :  5.999  69.697   1707
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 13.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 16.32 %
    Favored  : 81.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.33 (0.22), residues: 1562
  helix:  0.66 (0.19), residues: 716
  sheet: -0.49 (0.28), residues: 319
  loop : -1.12 (0.29), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 625 
 TYR   0.014   0.001   TYR B 125 
 PHE   0.022   0.001   PHE A 602 
 TRP   0.012   0.001   TRP A 665 
 HIS   0.005   0.001   HIS B 152 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.13 (12817)
  covalent geometry    : angle       0.72241 /  0.35 (17388)
  hydrogen bonds       : bond        0.03462 /  2.38 (  688)
  hydrogen bonds       : angle       5.26669 /  3.72 ( 1998)
  Misc. bond           : bond        0.20599 / 12.87 (    2)

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

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

  3124 Ramachandran restraints generated.
    1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3124 Ramachandran restraints generated.
    1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 72
  time to evaluate  : 0.537 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  323 ASN cc_start: 0.9619 (m110) cc_final: 0.9299 (p0)
REVERT: A  389 MET cc_start: 0.8722 (tmm) cc_final: 0.8201 (tmm)
REVERT: A  698 MET cc_start: 0.9466 (mpp) cc_final: 0.9204 (mpp)
REVERT: B  139 GLN cc_start: 0.9169 (OUTLIER) cc_final: 0.8820 (tm-30)
REVERT: B  253 PHE cc_start: 0.8250 (m-80) cc_final: 0.7940 (m-80)
REVERT: B  419 VAL cc_start: 0.8889 (OUTLIER) cc_final: 0.8423 (p)
REVERT: B  772 MET cc_start: 0.9612 (mtm) cc_final: 0.9121 (ptp)
  outliers start: 29
  outliers final: 19
  residues processed: 95
  average time/residue: 0.0904
  time to fit residues: 14.0156
Evaluate side-chains
  90 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 69
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  306 ASN
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  420 ASP
Chi-restraints excluded: chain A residue  597 VAL
Chi-restraints excluded: chain A residue  615 ILE
Chi-restraints excluded: chain A residue  654 LEU
Chi-restraints excluded: chain B residue  139 GLN
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  252 THR
Chi-restraints excluded: chain B residue  414 VAL
Chi-restraints excluded: chain B residue  419 VAL
Chi-restraints excluded: chain B residue  452 ASP
Chi-restraints excluded: chain B residue  640 LEU
Chi-restraints excluded: chain B residue  685 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 0 optimal weight:   30.0000
   chunk 38 optimal weight:    3.9990
   chunk 126 optimal weight:    0.0970
   chunk 109 optimal weight:    0.6980
   chunk 89 optimal weight:    5.9990
   chunk 31 optimal weight:    6.9990
   chunk 50 optimal weight:    5.9990
   chunk 144 optimal weight:    0.6980
   chunk 154 optimal weight:    0.3980
   chunk 65 optimal weight:    6.9990
   chunk 155 optimal weight:    3.9990
   overall best weight:    1.1780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 343 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 = 0.3717 r_free = 0.3717 target = 0.067318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.044496 restraints weight = 96381.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.043804 restraints weight = 76321.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.044265 restraints weight = 60825.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.045023 restraints weight = 51816.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.044969 restraints weight = 41749.913|
|-----------------------------------------------------------------------------|
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.4032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.275  12819  Z= 0.149
  Angle     :  0.721   9.353  17388  Z= 0.349
  Chirality :  0.044   0.178   1922
  Planarity :  0.005   0.047   2261
  Dihedral  :  5.950  69.944   1707
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 13.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 16.40 %
    Favored  : 81.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.23 (0.22), residues: 1562
  helix:  0.76 (0.19), residues: 717
  sheet: -0.48 (0.28), residues: 312
  loop : -1.07 (0.29), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 625 
 TYR   0.010   0.001   TYR B 454 
 PHE   0.025   0.002   PHE B 537 
 TRP   0.017   0.001   TRP A 665 
 HIS   0.004   0.001   HIS B 152 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00333 /  0.15 (12817)
  covalent geometry    : angle       0.72058 /  0.35 (17388)
  hydrogen bonds       : bond        0.03418 /  2.38 (  688)
  hydrogen bonds       : angle       5.27051 /  3.71 ( 1998)
  Misc. bond           : bond        0.19592 / 12.23 (    2)

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

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

  3124 Ramachandran restraints generated.
    1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3124 Ramachandran restraints generated.
    1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 68
  time to evaluate  : 0.534 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  308 MET cc_start: 0.9263 (tpp) cc_final: 0.9009 (tpp)
REVERT: A  323 ASN cc_start: 0.9440 (m110) cc_final: 0.9163 (p0)
REVERT: A  389 MET cc_start: 0.8761 (tmm) cc_final: 0.8234 (tmm)
REVERT: A  601 ARG cc_start: 0.9385 (OUTLIER) cc_final: 0.9087 (ttp-110)
REVERT: A  698 MET cc_start: 0.9391 (mpp) cc_final: 0.9169 (mpp)
REVERT: B  139 GLN cc_start: 0.9282 (OUTLIER) cc_final: 0.8863 (tm-30)
REVERT: B  491 MET cc_start: 0.9134 (tpp) cc_final: 0.8157 (tpp)
REVERT: B  772 MET cc_start: 0.9603 (mtm) cc_final: 0.9124 (ptp)
REVERT: B  799 MET cc_start: 0.8955 (ttt) cc_final: 0.8420 (ptm)
  outliers start: 27
  outliers final: 20
  residues processed: 89
  average time/residue: 0.0976
  time to fit residues: 13.8542
Evaluate side-chains
  90 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 68
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  306 ASN
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  420 ASP
Chi-restraints excluded: chain A residue  597 VAL
Chi-restraints excluded: chain A residue  601 ARG
Chi-restraints excluded: chain A residue  615 ILE
Chi-restraints excluded: chain A residue  654 LEU
Chi-restraints excluded: chain B residue  139 GLN
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  252 THR
Chi-restraints excluded: chain B residue  414 VAL
Chi-restraints excluded: chain B residue  452 ASP
Chi-restraints excluded: chain B residue  640 LEU
Chi-restraints excluded: chain B residue  685 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 18 optimal weight:    9.9990
   chunk 146 optimal weight:    4.9990
   chunk 127 optimal weight:    0.9980
   chunk 152 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 9 optimal weight:    6.9990
   chunk 76 optimal weight:    0.9990
   chunk 86 optimal weight:    9.9990
   chunk 29 optimal weight:   10.0000
   chunk 80 optimal weight:    9.9990
   chunk 54 optimal weight:    0.9990
   overall best weight:    0.9584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 343 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 = 0.3720 r_free = 0.3720 target = 0.067520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.044212 restraints weight = 97534.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.043573 restraints weight = 76384.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.044130 restraints weight = 61528.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.044268 restraints weight = 52232.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.044518 restraints weight = 47030.936|
|-----------------------------------------------------------------------------|
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.4190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.256  12819  Z= 0.138
  Angle     :  0.731  12.038  17388  Z= 0.352
  Chirality :  0.044   0.166   1922
  Planarity :  0.005   0.046   2261
  Dihedral  :  5.916  69.664   1707
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 13.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 16.40 %
    Favored  : 81.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.18 (0.22), residues: 1562
  helix:  0.81 (0.19), residues: 720
  sheet: -0.46 (0.28), residues: 315
  loop : -1.06 (0.29), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 625 
 TYR   0.008   0.001   TYR B 454 
 PHE   0.030   0.002   PHE B 537 
 TRP   0.016   0.001   TRP A 665 
 HIS   0.004   0.001   HIS B 152 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00311 /  0.14 (12817)
  covalent geometry    : angle       0.73082 /  0.35 (17388)
  hydrogen bonds       : bond        0.03358 /  2.33 (  688)
  hydrogen bonds       : angle       5.20449 /  3.65 ( 1998)
  Misc. bond           : bond        0.18160 / 11.35 (    2)

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

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

  3124 Ramachandran restraints generated.
    1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3124 Ramachandran restraints generated.
    1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 69
  time to evaluate  : 0.494 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  308 MET cc_start: 0.9303 (tpp) cc_final: 0.9074 (tpp)
REVERT: A  323 ASN cc_start: 0.9465 (m110) cc_final: 0.9177 (p0)
REVERT: A  389 MET cc_start: 0.8795 (tmm) cc_final: 0.8545 (tpp)
REVERT: A  601 ARG cc_start: 0.9391 (OUTLIER) cc_final: 0.9048 (ttp-110)
REVERT: A  698 MET cc_start: 0.9425 (mpp) cc_final: 0.9143 (mpp)
REVERT: B  139 GLN cc_start: 0.9300 (OUTLIER) cc_final: 0.9075 (pp30)
REVERT: B  253 PHE cc_start: 0.8471 (m-80) cc_final: 0.8242 (m-80)
REVERT: B  491 MET cc_start: 0.9249 (tpp) cc_final: 0.8341 (tpp)
REVERT: B  772 MET cc_start: 0.9632 (mtm) cc_final: 0.9144 (ptp)
REVERT: B  799 MET cc_start: 0.8995 (ttt) cc_final: 0.8453 (ptm)
  outliers start: 27
  outliers final: 21
  residues processed: 92
  average time/residue: 0.0953
  time to fit residues: 14.0094
Evaluate side-chains
  92 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 69
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  188 GLN
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  306 ASN
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  420 ASP
Chi-restraints excluded: chain A residue  597 VAL
Chi-restraints excluded: chain A residue  601 ARG
Chi-restraints excluded: chain A residue  615 ILE
Chi-restraints excluded: chain A residue  654 LEU
Chi-restraints excluded: chain A residue  711 PHE
Chi-restraints excluded: chain B residue  139 GLN
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  252 THR
Chi-restraints excluded: chain B residue  414 VAL
Chi-restraints excluded: chain B residue  452 ASP
Chi-restraints excluded: chain B residue  597 VAL
Chi-restraints excluded: chain B residue  640 LEU
Chi-restraints excluded: chain B residue  685 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 120 optimal weight:    2.9990
   chunk 137 optimal weight:    0.5980
   chunk 123 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 81 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 79 optimal weight:    7.9990
   chunk 3 optimal weight:   20.0000
   chunk 101 optimal weight:    2.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 343 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 = 0.3714 r_free = 0.3714 target = 0.067102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.043801 restraints weight = 98934.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.043002 restraints weight = 77845.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.043345 restraints weight = 62338.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.043858 restraints weight = 53621.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.043949 restraints weight = 46554.978|
|-----------------------------------------------------------------------------|
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.4320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.240  12819  Z= 0.154
  Angle     :  0.735  10.998  17388  Z= 0.354
  Chirality :  0.044   0.153   1922
  Planarity :  0.005   0.046   2261
  Dihedral  :  5.908  69.434   1707
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 14.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 16.62 %
    Favored  : 81.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.17 (0.22), residues: 1562
  helix:  0.79 (0.19), residues: 720
  sheet: -0.44 (0.29), residues: 315
  loop : -1.02 (0.29), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 625 
 TYR   0.009   0.001   TYR B 454 
 PHE   0.022   0.002   PHE A 602 
 TRP   0.018   0.001   TRP A 665 
 HIS   0.004   0.001   HIS B 152 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00343 /  0.15 (12817)
  covalent geometry    : angle       0.73515 /  0.35 (17388)
  hydrogen bonds       : bond        0.03361 /  2.34 (  688)
  hydrogen bonds       : angle       5.22747 /  3.67 ( 1998)
  Misc. bond           : bond        0.16957 / 10.60 (    2)

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

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

  3124 Ramachandran restraints generated.
    1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3124 Ramachandran restraints generated.
    1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 69
  time to evaluate  : 0.485 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  308 MET cc_start: 0.9296 (tpp) cc_final: 0.9058 (tpp)
REVERT: A  323 ASN cc_start: 0.9389 (m110) cc_final: 0.9162 (p0)
REVERT: A  389 MET cc_start: 0.8787 (tmm) cc_final: 0.8238 (tmm)
REVERT: A  601 ARG cc_start: 0.9358 (OUTLIER) cc_final: 0.9031 (ttp-110)
REVERT: A  698 MET cc_start: 0.9431 (mpp) cc_final: 0.9168 (mpp)
REVERT: A  711 PHE cc_start: 0.9094 (OUTLIER) cc_final: 0.8189 (m-80)
REVERT: B  139 GLN cc_start: 0.9277 (OUTLIER) cc_final: 0.8864 (tm-30)
REVERT: B  273 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7737 (tpt)
REVERT: B  491 MET cc_start: 0.9260 (tpp) cc_final: 0.8361 (tpp)
REVERT: B  545 MET cc_start: 0.9068 (tmm) cc_final: 0.8867 (ppp)
REVERT: B  772 MET cc_start: 0.9608 (mtm) cc_final: 0.9115 (ptp)
REVERT: B  799 MET cc_start: 0.8998 (ttt) cc_final: 0.8469 (ptm)
  outliers start: 24
  outliers final: 20
  residues processed: 89
  average time/residue: 0.0967
  time to fit residues: 13.6644
Evaluate side-chains
  93 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 69
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  188 GLN
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  306 ASN
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  420 ASP
Chi-restraints excluded: chain A residue  597 VAL
Chi-restraints excluded: chain A residue  601 ARG
Chi-restraints excluded: chain A residue  615 ILE
Chi-restraints excluded: chain A residue  654 LEU
Chi-restraints excluded: chain A residue  711 PHE
Chi-restraints excluded: chain B residue  139 GLN
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  252 THR
Chi-restraints excluded: chain B residue  273 MET
Chi-restraints excluded: chain B residue  414 VAL
Chi-restraints excluded: chain B residue  452 ASP
Chi-restraints excluded: chain B residue  597 VAL
Chi-restraints excluded: chain B residue  640 LEU
Chi-restraints excluded: chain B residue  685 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 146 optimal weight:    5.9990
   chunk 51 optimal weight:    0.0670
   chunk 36 optimal weight:    1.9990
   chunk 4 optimal weight:   40.0000
   chunk 138 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9990
   chunk 32 optimal weight:    4.9990
   chunk 3 optimal weight:   10.0000
   chunk 112 optimal weight:    0.6980
   chunk 63 optimal weight:    5.9990
   overall best weight:    0.8922

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 343 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 = 0.3721 r_free = 0.3721 target = 0.067468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.044823 restraints weight = 97895.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.045114 restraints weight = 76687.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.044599 restraints weight = 59246.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.044984 restraints weight = 52168.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.045049 restraints weight = 45154.298|
|-----------------------------------------------------------------------------|
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.4455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.227  12819  Z= 0.135
  Angle     :  0.730   9.872  17388  Z= 0.351
  Chirality :  0.044   0.162   1922
  Planarity :  0.005   0.047   2261
  Dihedral  :  5.888  71.393   1707
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 13.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 16.84 %
    Favored  : 81.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.07 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.14 (0.22), residues: 1562
  helix:  0.81 (0.20), residues: 719
  sheet: -0.41 (0.29), residues: 324
  loop : -1.03 (0.29), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 625 
 TYR   0.008   0.001   TYR B 415 
 PHE   0.022   0.002   PHE A 602 
 TRP   0.016   0.001   TRP A 665 
 HIS   0.004   0.001   HIS B 152 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00302 /  0.13 (12817)
  covalent geometry    : angle       0.72957 /  0.35 (17388)
  hydrogen bonds       : bond        0.03272 /  2.27 (  688)
  hydrogen bonds       : angle       5.16780 /  3.63 ( 1998)
  Misc. bond           : bond        0.16046 / 10.03 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2283.16 seconds
wall clock time: 40 minutes 18.13 seconds (2418.13 seconds total)