Starting phenix.real_space_refine
on Thu Aug  6 16:15:08 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lox_63262/08_2026/9lox_63262.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lox_63262/08_2026/9lox_63262.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9lox_63262/08_2026/9lox_63262.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lox_63262/08_2026/9lox_63262.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lox_63262/08_2026/9lox_63262.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lox_63262/08_2026/9lox_63262.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     284      5.49       5
     S      19      5.16       5
     C    9216      2.51       5
     N    2934      2.21       5
     O    3520      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 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: 15973
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 823
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 101, 823
          Classifications: {'peptide': 101}
          Link IDs: {'PTRANS': 3, 'TRANS': 97}
    Chain: "B"
      Number of atoms: 636
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 636
          Classifications: {'peptide': 79}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "C"
      Number of atoms: 730
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 730
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 4, 'TRANS': 90}
    Chain: "D"
      Number of atoms: 734
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 734
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 783
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "F"
      Number of atoms: 641
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 641
          Classifications: {'peptide': 80}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "G"
      Number of atoms: 804
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 804
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 5, 'TRANS': 99}
    Chain: "H"
      Number of atoms: 714
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 714
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
    Chain: "I"
      Number of atoms: 2894
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 142, 2894
          Classifications: {'DNA': 142}
          Link IDs: {'rna3p': 141}
    Chain: "J"
      Number of atoms: 2928
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 142, 2928
          Classifications: {'DNA': 142}
          Link IDs: {'rna3p': 141}
    Chain: "K"
      Number of atoms: 4286
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 528, 4286
          Classifications: {'peptide': 528}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 24, 'TRANS': 503}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 3.58, per 1000 atoms: 0.22
  Number of scatterers: 15973
  At special positions: 0
  Unit cell: (122.96, 128.26, 135.68, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      19     16.00
     P     284     15.00
     O    3520      8.00
     N    2934      7.00
     C    9216      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.33
  Conformation dependent library (CDL) restraints added in 567.9 milliseconds
  

  2494 Ramachandran restraints generated.
    1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2382

  Finding SS restraints...
    Secondary structure from input PDB file:
      61 helices and 13 sheets defined
      67.5% alpha, 5.6% beta
      141 base pairs and 251 stacking pairs defined.
    Time for finding SS restraints: 2.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 56
    Processing helix  chain 'A' and resid 64 through 78
      removed outlier: 4.071A  pdb=" N   ASP A  78 " --> pdb=" O   GLU A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 115
      removed outlier: 3.673A  pdb=" N   ALA A 115 " --> pdb=" O   CYS A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 132
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.743A  pdb=" N   GLN B  27 " --> pdb=" O   ASP B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.886A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.521A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.397A  pdb=" N   VAL C  49 " --> pdb=" O   SER C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 89
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 41 through 53
      removed outlier: 3.549A  pdb=" N   LYS D  47 " --> pdb=" O   SER D  43 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 59 through 88
    Processing helix  chain 'D' and resid 94 through 106
    Processing helix  chain 'D' and resid 107 through 130
      removed outlier: 4.186A  pdb=" N   GLN D 130 " --> pdb=" O   THR D 126 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 43 through 58
      removed outlier: 3.977A  pdb=" N   VAL E  47 " --> pdb=" O   LYS E  43 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   ALA E  48 " --> pdb=" O   PRO E  44 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 64 through 78
      removed outlier: 4.027A  pdb=" N   ASP E  78 " --> pdb=" O   GLU E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 86 through 115
      removed outlier: 3.935A  pdb=" N   ALA E 115 " --> pdb=" O   CYS E 111 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 121 through 132
    Processing helix  chain 'F' and resid 24 through 29
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.969A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.429A  pdb=" N   VAL G  49 " --> pdb=" O   SER G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 41 through 53
    Processing helix  chain 'H' and resid 59 through 88
    Processing helix  chain 'H' and resid 94 through 106
    Processing helix  chain 'H' and resid 107 through 129
    Processing helix  chain 'K' and resid 248 through 266
    Processing helix  chain 'K' and resid 300 through 304
    Processing helix  chain 'K' and resid 305 through 318
    Processing helix  chain 'K' and resid 335 through 349
      removed outlier: 3.994A  pdb=" N   ILE K 339 " --> pdb=" O   LYS K 335 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 364 through 376
    Processing helix  chain 'K' and resid 427 through 438
    Processing helix  chain 'K' and resid 446 through 457
      removed outlier: 5.132A  pdb=" N   LYS K 454 " --> pdb=" O   ARG K 450 " (cutoff:3.500A)
      removed outlier: 5.275A  pdb=" N   HIS K 455 " --> pdb=" O   ILE K 451 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 468 through 472
    Processing helix  chain 'K' and resid 477 through 485
    Processing helix  chain 'K' and resid 503 through 514
      removed outlier: 3.649A  pdb=" N   SER K 508 " --> pdb=" O   THR K 504 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   LEU K 509 " --> pdb=" O   GLU K 505 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   PHE K 512 " --> pdb=" O   SER K 508 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 520 through 535
      removed outlier: 4.949A  pdb=" N   ILE K 530 " --> pdb=" O   ASN K 526 " (cutoff:3.500A)
      Proline residue:  K 531  - end of helix
    Processing helix  chain 'K' and resid 541 through 560
    Processing helix  chain 'K' and resid 567 through 572
    Processing helix  chain 'K' and resid 588 through 601
    Processing helix  chain 'K' and resid 602 through 609
    Processing helix  chain 'K' and resid 614 through 618
    Processing helix  chain 'K' and resid 620 through 625
    Processing helix  chain 'K' and resid 628 through 632
      removed outlier: 3.523A  pdb=" N   VAL K 631 " --> pdb=" O   PRO K 628 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 635 through 640
    Processing helix  chain 'K' and resid 647 through 650
    Processing helix  chain 'K' and resid 651 through 668
      removed outlier: 3.743A  pdb=" N   GLN K 655 " --> pdb=" O   SER K 651 " (cutoff:3.500A)
      removed outlier: 5.063A  pdb=" N   GLU K 662 " --> pdb=" O   LYS K 658 " (cutoff:3.500A)
      removed outlier: 6.156A  pdb=" N   LEU K 663 " --> pdb=" O   LYS K 659 " (cutoff:3.500A)
      removed outlier: 4.484A  pdb=" N   TRP K 664 " --> pdb=" O   LEU K 660 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 677 through 695
      removed outlier: 3.513A  pdb=" N   LEU K 681 " --> pdb=" O   THR K 677 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 695 through 700
    Processing helix  chain 'K' and resid 716 through 728
      removed outlier: 3.757A  pdb=" N   SER K 720 " --> pdb=" O   GLY K 716 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 738 through 744
    Processing helix  chain 'K' and resid 761 through 770
      removed outlier: 3.794A  pdb=" N   ASP K 765 " --> pdb=" O   ASN K 761 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 790 through 812
    Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85
      removed outlier: 7.729A  pdb=" N   ARG A  84 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.427A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.398A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  93 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102
    Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85
      removed outlier: 7.244A  pdb=" N   ARG E  84 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 119 through 120
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.365A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  93 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'K' and resid 288 through 289
    Processing sheet with id=AB3, first strand: chain 'K' and resid 381 through 383
      removed outlier: 6.122A  pdb=" N   VAL K 382 " --> pdb=" O   ILE K 443 " (cutoff:3.500A)
      removed outlier: 8.409A  pdb=" N   THR K 445 " --> pdb=" O   VAL K 382 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   VAL K 359 " --> pdb=" O   ILE K 465 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   ALA K 464 " --> pdb=" O   VAL K 492 " (cutoff:3.500A)
      removed outlier: 8.140A  pdb=" N   LEU K 494 " --> pdb=" O   ALA K 464 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   LEU K 466 " --> pdb=" O   LEU K 494 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   LEU K 327 " --> pdb=" O   ILE K 493 " (cutoff:3.500A)
      removed outlier: 6.241A  pdb=" N   ILE K 326 " --> pdb=" O   LEU K 564 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'K' and resid 578 through 585
      removed outlier: 6.771A  pdb=" N   VAL K 753 " --> pdb=" O   TYR K 784 " (cutoff:3.500A)
      removed outlier: 8.138A  pdb=" N   LEU K 786 " --> pdb=" O   VAL K 753 " (cutoff:3.500A)
      removed outlier: 7.051A  pdb=" N   ILE K 755 " --> pdb=" O   LEU K 786 " (cutoff:3.500A)
      removed outlier: 8.814A  pdb=" N   ILE K 788 " --> pdb=" O   ILE K 755 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   LEU K 672 " --> pdb=" O   ILE K 754 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   THR K 737 " --> pdb=" O   MET K 709 " (cutoff:3.500A)

    611 hydrogen bonds defined for protein.
    1791 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      362 hydrogen bonds
      724 hydrogen bond angles
      0 basepair planarities
      141 basepair parallelities
      251 stacking parallelities
  Total time for adding SS restraints: 3.75

  Time building geometry restraints manager: 1.88 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 3424
        1.33 -     1.45: 4778
        1.45 -     1.57: 8058
        1.57 -     1.69: 566
        1.69 -     1.81: 29
  Bond restraints: 16855
  Sorted by residual:
  bond pdb=" C3'  DT J  14 "
       pdb=" C2'  DT J  14 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.09e+01
  bond pdb=" C3'  DC I  94 "
       pdb=" C2'  DC I  94 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.02e+01
  bond pdb=" C3'  DG J  51 "
       pdb=" C2'  DG J  51 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 1.01e+01
  bond pdb=" C3'  DA J  13 "
       pdb=" C2'  DA J  13 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 9.80e+00
  bond pdb=" C3'  DT J 139 "
       pdb=" C2'  DT J 139 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 9.73e+00
  ... (remaining 16850 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.86: 23017
        1.86 -     3.73: 911
        3.73 -     5.59: 50
        5.59 -     7.45: 9
        7.45 -     9.32: 7
  Bond angle restraints: 23994
  Sorted by residual:
  angle pdb=" O4'  DA I  90 "
        pdb=" C4'  DA I  90 "
        pdb=" C3'  DA I  90 "
      ideal   model   delta    sigma   weight residual
     106.00  103.13    2.87 6.00e-01 2.78e+00 2.29e+01
  angle pdb=" N3   DT J  23 "
        pdb=" C4   DT J  23 "
        pdb=" O4   DT J  23 "
      ideal   model   delta    sigma   weight residual
     119.90  122.61   -2.71 6.00e-01 2.78e+00 2.03e+01
  angle pdb=" N3   DT J  12 "
        pdb=" C4   DT J  12 "
        pdb=" O4   DT J  12 "
      ideal   model   delta    sigma   weight residual
     119.90  122.53   -2.63 6.00e-01 2.78e+00 1.92e+01
  angle pdb=" N3   DT J  82 "
        pdb=" C4   DT J  82 "
        pdb=" O4   DT J  82 "
      ideal   model   delta    sigma   weight residual
     119.90  122.52   -2.62 6.00e-01 2.78e+00 1.90e+01
  angle pdb=" N3   DT I 104 "
        pdb=" C4   DT I 104 "
        pdb=" O4   DT I 104 "
      ideal   model   delta    sigma   weight residual
     119.90  122.51   -2.61 6.00e-01 2.78e+00 1.89e+01
  ... (remaining 23989 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 6606
       17.97 -    35.93: 1335
       35.93 -    53.90: 1132
       53.90 -    71.87: 304
       71.87 -    89.83: 22
  Dihedral angle restraints: 9399
    sinusoidal: 5712
      harmonic: 3687
  Sorted by residual:
  dihedral pdb=" CA  ARG K 427 "
           pdb=" C   ARG K 427 "
           pdb=" N   VAL K 428 "
           pdb=" CA  VAL K 428 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.50  -22.50     0      5.00e+00 4.00e-02 2.03e+01
  dihedral pdb=" CA  PHE K 734 "
           pdb=" C   PHE K 734 "
           pdb=" N   LEU K 735 "
           pdb=" CA  LEU K 735 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.63   21.37     0      5.00e+00 4.00e-02 1.83e+01
  dihedral pdb=" CA  LEU K 743 "
           pdb=" C   LEU K 743 "
           pdb=" N   GLY K 744 "
           pdb=" CA  GLY K 744 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.25  -18.75     0      5.00e+00 4.00e-02 1.41e+01
  ... (remaining 9396 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.120: 2693
       0.120 -    0.240: 28
       0.240 -    0.360: 0
       0.360 -    0.481: 0
       0.481 -    0.601: 2
  Chirality restraints: 2723
  Sorted by residual:
  chirality pdb=" P    DG I   5 "
            pdb=" OP1  DG I   5 "
            pdb=" OP2  DG I   5 "
            pdb=" O5'  DG I   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.94   -0.60 2.00e-01 2.50e+01 9.02e+00
  chirality pdb=" P    DT J 142 "
            pdb=" OP1  DT J 142 "
            pdb=" OP2  DT J 142 "
            pdb=" O5'  DT J 142 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.91   -0.57 2.00e-01 2.50e+01 8.17e+00
  chirality pdb=" CB  ILE K 289 "
            pdb=" CA  ILE K 289 "
            pdb=" CG1 ILE K 289 "
            pdb=" CG2 ILE K 289 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.18 2.00e-01 2.50e+01 8.23e-01
  ... (remaining 2720 not shown)

  Planarity restraints: 2047
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU K 296 "    0.049 5.00e-02 4.00e+02   7.44e-02 8.86e+00
        pdb=" N   PRO K 297 "   -0.129 5.00e-02 4.00e+02
        pdb=" CA  PRO K 297 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO K 297 "    0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC I 142 "    0.033 2.00e-02 2.50e+03   1.61e-02 5.84e+00
        pdb=" N1   DC I 142 "   -0.029 2.00e-02 2.50e+03
        pdb=" C2   DC I 142 "    0.000 2.00e-02 2.50e+03
        pdb=" O2   DC I 142 "   -0.010 2.00e-02 2.50e+03
        pdb=" N3   DC I 142 "    0.006 2.00e-02 2.50e+03
        pdb=" C4   DC I 142 "    0.005 2.00e-02 2.50e+03
        pdb=" N4   DC I 142 "    0.011 2.00e-02 2.50e+03
        pdb=" C5   DC I 142 "   -0.005 2.00e-02 2.50e+03
        pdb=" C6   DC I 142 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE K 734 "    0.022 2.00e-02 2.50e+03   1.56e-02 4.28e+00
        pdb=" CG  PHE K 734 "   -0.033 2.00e-02 2.50e+03
        pdb=" CD1 PHE K 734 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 PHE K 734 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE1 PHE K 734 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE K 734 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE K 734 "    0.010 2.00e-02 2.50e+03
  ... (remaining 2044 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1419
        2.74 -     3.28: 15158
        3.28 -     3.82: 29917
        3.82 -     4.36: 35096
        4.36 -     4.90: 53029
  Nonbonded interactions: 134619
  Sorted by model distance:
  nonbonded pdb=" OG1 THR E  81 "
            pdb=" OD1 ASP E  82 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" OD1 ASP K 723 "
            pdb=" ND2 ASN K 727 "
     model   vdw
     2.219 3.120
  nonbonded pdb=" OD2 ASP A 107 "
            pdb=" NH1 ARG A 132 "
     model   vdw
     2.258 3.120
  nonbonded pdb=" NZ  LYS D  90 "
            pdb=" OE2 GLU D  97 "
     model   vdw
     2.272 3.120
  nonbonded pdb=" OH  TYR B  98 "
            pdb=" OD2 ASP H  72 "
     model   vdw
     2.284 3.040
  ... (remaining 134614 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 40 through 134)
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and resid 23 through 101)
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 15 through 109)
}
ncs_group {
  reference = (chain 'D' and resid 38 through 129)
  selection = chain 'H'
}

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=0.00 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:             1.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     17.970
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  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:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057  16855  Z= 0.467
  Angle     :  0.765   9.318  23994  Z= 0.617
  Chirality :  0.048   0.601   2723
  Planarity :  0.005   0.074   2047
  Dihedral  : 25.887  89.833   7017
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.49 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  : 11.43 %
    Favored  : 88.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.27 (0.24), residues: 1247
  helix:  1.60 (0.18), residues: 794
  sheet:  0.19 (0.65), residues: 73
  loop : -0.59 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG C  35 
 TYR   0.009   0.001   TYR G  57 
 PHE   0.033   0.002   PHE K 734 
 TRP   0.016   0.002   TRP K 259 
 HIS   0.010   0.001   HIS C  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00543 /  0.47 (16855)
  covalent geometry    : angle       0.76526 /  0.62 (23994)
  hydrogen bonds       : bond        0.12973 /  9.07 (  973)
  hydrogen bonds       : angle       4.67510 /  3.40 ( 2515)

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

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

  2494 Ramachandran restraints generated.
    1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2494 Ramachandran restraints generated.
    1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  331 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 326
  time to evaluate  : 0.611 
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: G   94 ASN cc_start: 0.8721 (t0) cc_final: 0.8239 (t0)
REVERT: K  447 VAL cc_start: 0.6793 (t) cc_final: 0.6331 (t)
REVERT: K  486 LEU cc_start: 0.8003 (mt) cc_final: 0.7750 (pt)
REVERT: K  563 LEU cc_start: 0.7024 (tt) cc_final: 0.6769 (tt)
REVERT: K  611 LYS cc_start: 0.5559 (mttt) cc_final: 0.5282 (tppt)
  outliers start: 5
  outliers final: 3
  residues processed: 331
  average time/residue: 0.1841
  time to fit residues: 81.9356
Evaluate side-chains
  169 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 166
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  363 THR
Chi-restraints excluded: chain K residue  691 LEU
Chi-restraints excluded: chain K residue  732 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 98 optimal weight:   50.0000
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    0.0870
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:   20.0000
   chunk 77 optimal weight:   20.0000
   chunk 122 optimal weight:    4.9990
   chunk 91 optimal weight:   20.0000
   chunk 149 optimal weight:    4.9990
   overall best weight:    3.4166

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  84 GLN
D  88 ASN
E  86 GLN
E 121 GLN
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 104 GLN
K 634 HIS
** K 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 798 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.118538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.081224 restraints weight = 46833.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.082074 restraints weight = 24307.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.083030 restraints weight = 16162.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.083100 restraints weight = 12778.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.083274 restraints weight = 13630.597|
|-----------------------------------------------------------------------------|
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.2010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067  16855  Z= 0.238
  Angle     :  0.764   9.297  23994  Z= 0.424
  Chirality :  0.048   0.227   2723
  Planarity :  0.006   0.041   2047
  Dihedral  : 29.347  89.671   4501
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.89 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 14.99 %
    Favored  : 80.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.20 (0.23), residues: 1247
  helix:  1.61 (0.18), residues: 801
  sheet:  0.50 (0.66), residues: 71
  loop : -0.90 (0.31), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG C  35 
 TYR   0.023   0.002   TYR D  87 
 PHE   0.029   0.002   PHE K 734 
 TRP   0.014   0.002   TRP K 368 
 HIS   0.010   0.002   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00511 /  0.24 (16855)
  covalent geometry    : angle       0.76439 /  0.42 (23994)
  hydrogen bonds       : bond        0.05929 /  4.02 (  973)
  hydrogen bonds       : angle       4.16992 /  3.04 ( 2515)

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

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

  2494 Ramachandran restraints generated.
    1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2494 Ramachandran restraints generated.
    1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 170
  time to evaluate  : 0.484 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 GLU cc_start: 0.8437 (tp30) cc_final: 0.8224 (tp30)
REVERT: D  117 GLU cc_start: 0.8413 (tp30) cc_final: 0.8020 (tm-30)
REVERT: F   25 ASN cc_start: 0.8268 (m-40) cc_final: 0.8033 (m-40)
REVERT: H   60 GLN cc_start: 0.8505 (tm-30) cc_final: 0.8279 (tm-30)
REVERT: K  306 ASP cc_start: 0.7302 (OUTLIER) cc_final: 0.6904 (t0)
REVERT: K  468 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8220 (mp0)
REVERT: K  557 ASP cc_start: 0.8018 (m-30) cc_final: 0.7805 (p0)
REVERT: K  611 LYS cc_start: 0.5576 (mttt) cc_final: 0.5101 (tppt)
REVERT: K  736 LEU cc_start: 0.8925 (mp) cc_final: 0.8535 (mm)
  outliers start: 48
  outliers final: 21
  residues processed: 204
  average time/residue: 0.1452
  time to fit residues: 42.6688
Evaluate side-chains
  172 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 149
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain E residue   47 VAL
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   78 ILE
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue   85 LEU
Chi-restraints excluded: chain H residue  111 SER
Chi-restraints excluded: chain K residue  306 ASP
Chi-restraints excluded: chain K residue  327 LEU
Chi-restraints excluded: chain K residue  357 ILE
Chi-restraints excluded: chain K residue  369 CYS
Chi-restraints excluded: chain K residue  372 PHE
Chi-restraints excluded: chain K residue  449 LEU
Chi-restraints excluded: chain K residue  468 GLU
Chi-restraints excluded: chain K residue  503 LEU
Chi-restraints excluded: chain K residue  504 THR
Chi-restraints excluded: chain K residue  691 LEU
Chi-restraints excluded: chain K residue  775 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 143 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9990
   chunk 147 optimal weight:    9.9990
   chunk 120 optimal weight:   10.0000
   chunk 69 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 50 optimal weight:    0.7980
   overall best weight:    1.5586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E 121 GLN
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 767 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.118735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.081412 restraints weight = 47034.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.082537 restraints weight = 23487.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.083477 restraints weight = 15029.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.083932 restraints weight = 12365.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.083870 restraints weight = 12337.795|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.2295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064  16855  Z= 0.163
  Angle     :  0.662   9.344  23994  Z= 0.377
  Chirality :  0.045   0.246   2723
  Planarity :  0.005   0.055   2047
  Dihedral  : 29.371  89.713   4498
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 10.33
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.21 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 15.54 %
    Favored  : 81.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.35 (0.24), residues: 1247
  helix:  1.77 (0.18), residues: 808
  sheet:  0.52 (0.66), residues: 71
  loop : -0.99 (0.30), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG K 799 
 TYR   0.025   0.001   TYR C  57 
 PHE   0.037   0.002   PHE K 734 
 TRP   0.009   0.001   TRP K 368 
 HIS   0.008   0.001   HIS C  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00325 /  0.16 (16855)
  covalent geometry    : angle       0.66228 /  0.38 (23994)
  hydrogen bonds       : bond        0.05083 /  3.44 (  973)
  hydrogen bonds       : angle       3.85014 /  2.79 ( 2515)

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

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

  2494 Ramachandran restraints generated.
    1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2494 Ramachandran restraints generated.
    1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 161
  time to evaluate  : 0.476 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.8321 (m-10) cc_final: 0.8071 (m-10)
REVERT: C   56 GLU cc_start: 0.8202 (tt0) cc_final: 0.7961 (tt0)
REVERT: D  117 GLU cc_start: 0.8437 (tp30) cc_final: 0.8051 (tm-30)
REVERT: E   62 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8767 (mt)
REVERT: E   74 GLU cc_start: 0.7590 (tt0) cc_final: 0.6861 (tt0)
REVERT: E   98 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7157 (mt-10)
REVERT: F   25 ASN cc_start: 0.8297 (m-40) cc_final: 0.8010 (m110)
REVERT: H   60 GLN cc_start: 0.8489 (tm-30) cc_final: 0.8112 (tm-30)
REVERT: K  306 ASP cc_start: 0.7220 (OUTLIER) cc_final: 0.6883 (t0)
REVERT: K  767 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8497 (tp40)
  outliers start: 33
  outliers final: 14
  residues processed: 183
  average time/residue: 0.1322
  time to fit residues: 35.5812
Evaluate side-chains
  161 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 144
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain E residue   62 LEU
Chi-restraints excluded: chain E residue  113 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   16 SER
Chi-restraints excluded: chain G residue   78 ILE
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain K residue  306 ASP
Chi-restraints excluded: chain K residue  327 LEU
Chi-restraints excluded: chain K residue  357 ILE
Chi-restraints excluded: chain K residue  503 LEU
Chi-restraints excluded: chain K residue  521 LEU
Chi-restraints excluded: chain K residue  691 LEU
Chi-restraints excluded: chain K residue  767 GLN
Chi-restraints excluded: chain K residue  786 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 28 optimal weight:    6.9990
   chunk 149 optimal weight:    9.9990
   chunk 90 optimal weight:   20.0000
   chunk 14 optimal weight:    0.6980
   chunk 61 optimal weight:    5.9990
   chunk 138 optimal weight:   10.0000
   chunk 106 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   chunk 25 optimal weight:    5.9990
   chunk 54 optimal weight:    4.9990
   chunk 144 optimal weight:    9.9990
   overall best weight:    2.7186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E 121 GLN
** G  84 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 = 0.4232 r_free = 0.4232 target = 0.117062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.078112 restraints weight = 47214.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.080242 restraints weight = 22579.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.081589 restraints weight = 14928.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.082319 restraints weight = 12145.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.082609 restraints weight = 11041.996|
|-----------------------------------------------------------------------------|
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.2675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  16855  Z= 0.198
  Angle     :  0.679   8.974  23994  Z= 0.380
  Chirality :  0.045   0.222   2723
  Planarity :  0.005   0.051   2047
  Dihedral  : 29.424  88.836   4498
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.53 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 16.09 %
    Favored  : 79.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.32 (0.24), residues: 1247
  helix:  1.75 (0.18), residues: 805
  sheet:  0.37 (0.66), residues: 73
  loop : -0.96 (0.30), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG K 491 
 TYR   0.017   0.002   TYR C  57 
 PHE   0.029   0.001   PHE K 734 
 TRP   0.006   0.001   TRP K 760 
 HIS   0.008   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00417 /  0.20 (16855)
  covalent geometry    : angle       0.67943 /  0.38 (23994)
  hydrogen bonds       : bond        0.05266 /  3.57 (  973)
  hydrogen bonds       : angle       3.90129 /  2.83 ( 2515)

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

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

  2494 Ramachandran restraints generated.
    1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2494 Ramachandran restraints generated.
    1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 154
  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: symmetry clash
REVERT: C   56 GLU cc_start: 0.8232 (tt0) cc_final: 0.7806 (tt0)
REVERT: D  117 GLU cc_start: 0.8369 (tp30) cc_final: 0.8145 (tm-30)
REVERT: E   62 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8836 (mt)
REVERT: E   98 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7253 (mt-10)
REVERT: F   93 GLN cc_start: 0.8467 (mm-40) cc_final: 0.8242 (mm110)
REVERT: G   94 ASN cc_start: 0.9042 (t0) cc_final: 0.8665 (t0)
REVERT: K  306 ASP cc_start: 0.7223 (OUTLIER) cc_final: 0.6915 (t0)
REVERT: K  557 ASP cc_start: 0.8010 (m-30) cc_final: 0.7734 (p0)
  outliers start: 45
  outliers final: 28
  residues processed: 187
  average time/residue: 0.1330
  time to fit residues: 36.6863
Evaluate side-chains
  171 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 141
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   60 GLU
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   99 HIS
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain E residue   62 LEU
Chi-restraints excluded: chain E residue   66 LEU
Chi-restraints excluded: chain E residue  113 ILE
Chi-restraints excluded: chain E residue  125 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   16 SER
Chi-restraints excluded: chain G residue   78 ILE
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain H residue  111 SER
Chi-restraints excluded: chain K residue  306 ASP
Chi-restraints excluded: chain K residue  327 LEU
Chi-restraints excluded: chain K residue  357 ILE
Chi-restraints excluded: chain K residue  363 THR
Chi-restraints excluded: chain K residue  449 LEU
Chi-restraints excluded: chain K residue  503 LEU
Chi-restraints excluded: chain K residue  504 THR
Chi-restraints excluded: chain K residue  521 LEU
Chi-restraints excluded: chain K residue  570 ASP
Chi-restraints excluded: chain K residue  691 LEU
Chi-restraints excluded: chain K residue  786 LEU
Chi-restraints excluded: chain K residue  804 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 114 optimal weight:   10.0000
   chunk 78 optimal weight:   20.0000
   chunk 2 optimal weight:    6.9990
   chunk 59 optimal weight:    0.9990
   chunk 137 optimal weight:   30.0000
   chunk 35 optimal weight:   10.0000
   chunk 112 optimal weight:   20.0000
   chunk 100 optimal weight:    5.9990
   chunk 90 optimal weight:   20.0000
   chunk 26 optimal weight:    6.9990
   chunk 20 optimal weight:    0.0870
   overall best weight:    4.2166

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  88 ASN
E 121 GLN
F  75 HIS
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.114738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.075587 restraints weight = 47259.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.077533 restraints weight = 23131.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.078814 restraints weight = 15580.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.079481 restraints weight = 12754.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.079820 restraints weight = 11626.538|
|-----------------------------------------------------------------------------|
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.3141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.063  16855  Z= 0.265
  Angle     :  0.744   7.541  23994  Z= 0.408
  Chirality :  0.047   0.243   2723
  Planarity :  0.005   0.052   2047
  Dihedral  : 29.598  89.424   4498
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.85 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 17.28 %
    Favored  : 77.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.98 (0.23), residues: 1247
  helix:  1.49 (0.18), residues: 807
  sheet:  0.38 (0.66), residues: 73
  loop : -1.16 (0.31), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG K 450 
 TYR   0.027   0.002   TYR G  50 
 PHE   0.032   0.002   PHE K 734 
 TRP   0.007   0.001   TRP K 314 
 HIS   0.008   0.002   HIS C  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00577 /  0.27 (16855)
  covalent geometry    : angle       0.74384 /  0.41 (23994)
  hydrogen bonds       : bond        0.05971 /  4.04 (  973)
  hydrogen bonds       : angle       4.10298 /  2.98 ( 2515)

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

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

  2494 Ramachandran restraints generated.
    1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2494 Ramachandran restraints generated.
    1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 142
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   56 GLU cc_start: 0.8373 (tt0) cc_final: 0.7987 (tt0)
REVERT: D   60 GLN cc_start: 0.8725 (tm-30) cc_final: 0.8431 (tm-30)
REVERT: D   63 MET cc_start: 0.9116 (tpp) cc_final: 0.8661 (tpp)
REVERT: D  117 GLU cc_start: 0.8465 (tp30) cc_final: 0.8114 (tm-30)
REVERT: F   25 ASN cc_start: 0.8502 (m-40) cc_final: 0.8263 (m110)
REVERT: G   94 ASN cc_start: 0.9125 (t0) cc_final: 0.8752 (t0)
REVERT: H  109 GLU cc_start: 0.7570 (tm-30) cc_final: 0.7286 (tm-30)
REVERT: H  117 GLU cc_start: 0.7966 (tt0) cc_final: 0.7689 (tm-30)
REVERT: K  306 ASP cc_start: 0.7241 (OUTLIER) cc_final: 0.6880 (t0)
REVERT: K  371 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7940 (mm-30)
REVERT: K  486 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.6644 (mm)
REVERT: K  557 ASP cc_start: 0.8001 (m-30) cc_final: 0.7764 (p0)
REVERT: K  709 MET cc_start: 0.5543 (mpp) cc_final: 0.4994 (mpp)
REVERT: K  767 GLN cc_start: 0.9114 (tp40) cc_final: 0.8904 (pp30)
  outliers start: 55
  outliers final: 39
  residues processed: 183
  average time/residue: 0.1250
  time to fit residues: 34.3333
Evaluate side-chains
  177 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 136
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   60 GLU
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   87 ILE
Chi-restraints excluded: chain C residue   99 HIS
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain D residue  102 VAL
Chi-restraints excluded: chain E residue   47 VAL
Chi-restraints excluded: chain E residue   66 LEU
Chi-restraints excluded: chain E residue  110 LEU
Chi-restraints excluded: chain E residue  113 ILE
Chi-restraints excluded: chain E residue  121 GLN
Chi-restraints excluded: chain E residue  125 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   16 SER
Chi-restraints excluded: chain G residue   78 ILE
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain H residue  111 SER
Chi-restraints excluded: chain K residue  306 ASP
Chi-restraints excluded: chain K residue  327 LEU
Chi-restraints excluded: chain K residue  357 ILE
Chi-restraints excluded: chain K residue  363 THR
Chi-restraints excluded: chain K residue  387 ILE
Chi-restraints excluded: chain K residue  486 LEU
Chi-restraints excluded: chain K residue  503 LEU
Chi-restraints excluded: chain K residue  504 THR
Chi-restraints excluded: chain K residue  521 LEU
Chi-restraints excluded: chain K residue  570 ASP
Chi-restraints excluded: chain K residue  681 LEU
Chi-restraints excluded: chain K residue  691 LEU
Chi-restraints excluded: chain K residue  769 ARG
Chi-restraints excluded: chain K residue  786 LEU
Chi-restraints excluded: chain K residue  792 ILE
Chi-restraints excluded: chain K residue  804 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 141 optimal weight:    6.9990
   chunk 122 optimal weight:    5.9990
   chunk 58 optimal weight:    0.0970
   chunk 90 optimal weight:   20.0000
   chunk 27 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 128 optimal weight:   20.0000
   chunk 89 optimal weight:   20.0000
   chunk 82 optimal weight:   20.0000
   chunk 99 optimal weight:   20.0000
   chunk 95 optimal weight:   20.0000
   overall best weight:    3.3984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 121 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 = 0.3925 r_free = 0.3925 target = 0.106588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.065696 restraints weight = 49814.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.067808 restraints weight = 22950.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.069098 restraints weight = 15109.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.069811 restraints weight = 12205.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.069983 restraints weight = 10991.676|
|-----------------------------------------------------------------------------|
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.3335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.079  16855  Z= 0.220
  Angle     :  0.683   7.496  23994  Z= 0.381
  Chirality :  0.045   0.236   2723
  Planarity :  0.004   0.047   2047
  Dihedral  : 29.563  88.386   4498
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.45 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 19.01 %
    Favored  : 76.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.14 (0.24), residues: 1247
  helix:  1.63 (0.18), residues: 809
  sheet:  0.35 (0.65), residues: 73
  loop : -1.13 (0.31), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG K 450 
 TYR   0.033   0.002   TYR D  87 
 PHE   0.022   0.002   PHE K 706 
 TRP   0.008   0.001   TRP K 314 
 HIS   0.008   0.001   HIS C  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00473 /  0.22 (16855)
  covalent geometry    : angle       0.68345 /  0.38 (23994)
  hydrogen bonds       : bond        0.05455 /  3.66 (  973)
  hydrogen bonds       : angle       4.00471 /  2.89 ( 2515)

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

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

  2494 Ramachandran restraints generated.
    1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2494 Ramachandran restraints generated.
    1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 144
  time to evaluate  : 0.500 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   56 GLU cc_start: 0.8732 (tt0) cc_final: 0.8104 (tt0)
REVERT: D   60 GLN cc_start: 0.8862 (tm-30) cc_final: 0.8474 (tm-30)
REVERT: D  117 GLU cc_start: 0.8740 (tp30) cc_final: 0.8183 (tm-30)
REVERT: E  110 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8529 (tp)
REVERT: F   25 ASN cc_start: 0.8709 (m-40) cc_final: 0.8398 (m110)
REVERT: G   94 ASN cc_start: 0.9059 (t0) cc_final: 0.8699 (t0)
REVERT: H  117 GLU cc_start: 0.8263 (tt0) cc_final: 0.7721 (tm-30)
REVERT: K  306 ASP cc_start: 0.7135 (OUTLIER) cc_final: 0.6845 (t0)
REVERT: K  447 VAL cc_start: 0.6574 (t) cc_final: 0.6323 (t)
REVERT: K  557 ASP cc_start: 0.8159 (m-30) cc_final: 0.7862 (p0)
REVERT: K  709 MET cc_start: 0.6389 (mpp) cc_final: 0.6141 (mpp)
  outliers start: 44
  outliers final: 35
  residues processed: 177
  average time/residue: 0.1294
  time to fit residues: 34.0337
Evaluate side-chains
  174 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 137
  time to evaluate  : 0.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   60 GLU
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   99 HIS
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain D residue  102 VAL
Chi-restraints excluded: chain E residue   47 VAL
Chi-restraints excluded: chain E residue   66 LEU
Chi-restraints excluded: chain E residue  110 LEU
Chi-restraints excluded: chain E residue  113 ILE
Chi-restraints excluded: chain E residue  125 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain G residue   16 SER
Chi-restraints excluded: chain G residue   78 ILE
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain H residue  111 SER
Chi-restraints excluded: chain K residue  306 ASP
Chi-restraints excluded: chain K residue  327 LEU
Chi-restraints excluded: chain K residue  357 ILE
Chi-restraints excluded: chain K residue  363 THR
Chi-restraints excluded: chain K residue  449 LEU
Chi-restraints excluded: chain K residue  503 LEU
Chi-restraints excluded: chain K residue  504 THR
Chi-restraints excluded: chain K residue  521 LEU
Chi-restraints excluded: chain K residue  570 ASP
Chi-restraints excluded: chain K residue  681 LEU
Chi-restraints excluded: chain K residue  691 LEU
Chi-restraints excluded: chain K residue  786 LEU
Chi-restraints excluded: chain K residue  792 ILE
Chi-restraints excluded: chain K residue  804 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 17 optimal weight:    0.4980
   chunk 11 optimal weight:    0.8980
   chunk 134 optimal weight:    0.0030
   chunk 136 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9990
   chunk 130 optimal weight:    6.9990
   chunk 106 optimal weight:    6.9990
   chunk 95 optimal weight:   20.0000
   chunk 42 optimal weight:    2.9990
   chunk 141 optimal weight:   10.0000
   chunk 133 optimal weight:    5.9990
   overall best weight:    0.8794

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 121 GLN
K 527 GLN
** K 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.108344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.068768 restraints weight = 49482.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.070891 restraints weight = 23184.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.072220 restraints weight = 15346.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.072967 restraints weight = 12450.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.073320 restraints weight = 11255.251|
|-----------------------------------------------------------------------------|
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.3418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047  16855  Z= 0.136
  Angle     :  0.625  10.887  23994  Z= 0.354
  Chirality :  0.043   0.208   2723
  Planarity :  0.004   0.046   2047
  Dihedral  : 29.334  87.765   4498
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.05 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 20.38 %
    Favored  : 76.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.58 (0.24), residues: 1247
  helix:  1.98 (0.18), residues: 809
  sheet:  0.46 (0.66), residues: 73
  loop : -0.97 (0.31), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG K 739 
 TYR   0.028   0.001   TYR D  87 
 PHE   0.014   0.001   PHE K 706 
 TRP   0.008   0.001   TRP K 760 
 HIS   0.005   0.001   HIS C  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00250 /  0.14 (16855)
  covalent geometry    : angle       0.62473 /  0.35 (23994)
  hydrogen bonds       : bond        0.04629 /  3.10 (  973)
  hydrogen bonds       : angle       3.70720 /  2.68 ( 2515)

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

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

  2494 Ramachandran restraints generated.
    1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2494 Ramachandran restraints generated.
    1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 151
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   77 LYS cc_start: 0.9053 (mmtp) cc_final: 0.8714 (mttm)
REVERT: C   56 GLU cc_start: 0.8474 (tt0) cc_final: 0.7958 (tt0)
REVERT: C   92 GLU cc_start: 0.7471 (mp0) cc_final: 0.7263 (mp0)
REVERT: D   60 GLN cc_start: 0.8664 (tm-30) cc_final: 0.8336 (tm-30)
REVERT: D   63 MET cc_start: 0.9151 (tpp) cc_final: 0.8769 (tpp)
REVERT: D  117 GLU cc_start: 0.8593 (tp30) cc_final: 0.8303 (tm-30)
REVERT: E  110 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8588 (tp)
REVERT: F   25 ASN cc_start: 0.8610 (m-40) cc_final: 0.8345 (m110)
REVERT: F   27 GLN cc_start: 0.8790 (mp10) cc_final: 0.8020 (mp10)
REVERT: G   50 TYR cc_start: 0.8722 (t80) cc_final: 0.8511 (t80)
REVERT: G   94 ASN cc_start: 0.9072 (t0) cc_final: 0.8708 (t0)
REVERT: H  117 GLU cc_start: 0.8022 (tt0) cc_final: 0.7592 (tm-30)
REVERT: K  306 ASP cc_start: 0.7100 (OUTLIER) cc_final: 0.6846 (t0)
REVERT: K  557 ASP cc_start: 0.8122 (m-30) cc_final: 0.7819 (p0)
REVERT: K  709 MET cc_start: 0.6070 (mpp) cc_final: 0.5787 (mpp)
  outliers start: 34
  outliers final: 24
  residues processed: 174
  average time/residue: 0.1220
  time to fit residues: 31.6688
Evaluate side-chains
  163 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 137
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   60 GLU
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   87 ILE
Chi-restraints excluded: chain C residue   99 HIS
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain E residue   49 LEU
Chi-restraints excluded: chain E residue  110 LEU
Chi-restraints excluded: chain E residue  123 LYS
Chi-restraints excluded: chain E residue  125 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue   85 LEU
Chi-restraints excluded: chain K residue  306 ASP
Chi-restraints excluded: chain K residue  357 ILE
Chi-restraints excluded: chain K residue  363 THR
Chi-restraints excluded: chain K residue  503 LEU
Chi-restraints excluded: chain K residue  570 ASP
Chi-restraints excluded: chain K residue  681 LEU
Chi-restraints excluded: chain K residue  691 LEU
Chi-restraints excluded: chain K residue  786 LEU
Chi-restraints excluded: chain K residue  792 ILE
Chi-restraints excluded: chain K residue  804 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 140 optimal weight:    6.9990
   chunk 47 optimal weight:    0.6980
   chunk 46 optimal weight:    4.9990
   chunk 105 optimal weight:    9.9990
   chunk 65 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 55 optimal weight:    0.6980
   chunk 129 optimal weight:    5.9990
   chunk 108 optimal weight:    0.9990
   chunk 45 optimal weight:    0.6980
   chunk 148 optimal weight:   20.0000
   overall best weight:    1.0184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 732 ASN ** 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 = 0.3964 r_free = 0.3964 target = 0.108345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.068711 restraints weight = 49678.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.070886 restraints weight = 23241.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.072208 restraints weight = 15350.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.072951 restraints weight = 12455.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.073320 restraints weight = 11251.443|
|-----------------------------------------------------------------------------|
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.3533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  16855  Z= 0.137
  Angle     :  0.614  10.612  23994  Z= 0.348
  Chirality :  0.042   0.211   2723
  Planarity :  0.004   0.044   2047
  Dihedral  : 29.246  87.169   4498
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.13 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 20.66 %
    Favored  : 76.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.65 (0.24), residues: 1247
  helix:  2.05 (0.18), residues: 807
  sheet:  0.58 (0.67), residues: 73
  loop : -0.97 (0.31), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  35 
 TYR   0.024   0.001   TYR D  87 
 PHE   0.013   0.001   PHE K 706 
 TRP   0.008   0.001   TRP K 760 
 HIS   0.004   0.001   HIS C  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00261 /  0.14 (16855)
  covalent geometry    : angle       0.61416 /  0.35 (23994)
  hydrogen bonds       : bond        0.04548 /  3.04 (  973)
  hydrogen bonds       : angle       3.65481 /  2.64 ( 2515)

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

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

  2494 Ramachandran restraints generated.
    1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2494 Ramachandran restraints generated.
    1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 143
  time to evaluate  : 0.461 
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: B   77 LYS cc_start: 0.9055 (mmtp) cc_final: 0.8742 (mttm)
REVERT: C   56 GLU cc_start: 0.8516 (tt0) cc_final: 0.7976 (tt0)
REVERT: D   60 GLN cc_start: 0.8698 (tm-30) cc_final: 0.8348 (tm-30)
REVERT: D   63 MET cc_start: 0.9122 (tpp) cc_final: 0.8796 (tpp)
REVERT: D  117 GLU cc_start: 0.8577 (tp30) cc_final: 0.8279 (tm-30)
REVERT: E   60 GLU cc_start: 0.7542 (pm20) cc_final: 0.7304 (pm20)
REVERT: F   25 ASN cc_start: 0.8616 (m-40) cc_final: 0.8409 (m-40)
REVERT: G   50 TYR cc_start: 0.8743 (t80) cc_final: 0.8517 (t80)
REVERT: G   94 ASN cc_start: 0.9059 (t0) cc_final: 0.8698 (t0)
REVERT: H  117 GLU cc_start: 0.8051 (tt0) cc_final: 0.7587 (tm-30)
REVERT: K  306 ASP cc_start: 0.7014 (OUTLIER) cc_final: 0.6768 (t0)
REVERT: K  331 MET cc_start: 0.6896 (tpp) cc_final: 0.6254 (tpp)
REVERT: K  557 ASP cc_start: 0.8191 (m-30) cc_final: 0.7865 (p0)
REVERT: K  709 MET cc_start: 0.6089 (mpp) cc_final: 0.5809 (mpp)
  outliers start: 34
  outliers final: 27
  residues processed: 167
  average time/residue: 0.1332
  time to fit residues: 32.5472
Evaluate side-chains
  166 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 138
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   60 GLU
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   99 HIS
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain E residue   49 LEU
Chi-restraints excluded: chain E residue  125 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain K residue  306 ASP
Chi-restraints excluded: chain K residue  327 LEU
Chi-restraints excluded: chain K residue  357 ILE
Chi-restraints excluded: chain K residue  363 THR
Chi-restraints excluded: chain K residue  449 LEU
Chi-restraints excluded: chain K residue  494 LEU
Chi-restraints excluded: chain K residue  503 LEU
Chi-restraints excluded: chain K residue  521 LEU
Chi-restraints excluded: chain K residue  570 ASP
Chi-restraints excluded: chain K residue  681 LEU
Chi-restraints excluded: chain K residue  691 LEU
Chi-restraints excluded: chain K residue  769 ARG
Chi-restraints excluded: chain K residue  786 LEU
Chi-restraints excluded: chain K residue  792 ILE
Chi-restraints excluded: chain K residue  804 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 36 optimal weight:    0.8980
   chunk 136 optimal weight:   20.0000
   chunk 131 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 42 optimal weight:    0.5980
   chunk 21 optimal weight:    0.7980
   chunk 129 optimal weight:    8.9990
   chunk 38 optimal weight:    2.9990
   chunk 126 optimal weight:    9.9990
   chunk 145 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E  69 GLN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 732 ASN ** 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 = 0.3980 r_free = 0.3980 target = 0.109351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.069910 restraints weight = 49600.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.072125 restraints weight = 23339.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.073466 restraints weight = 15371.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.074195 restraints weight = 12445.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.074586 restraints weight = 11251.059|
|-----------------------------------------------------------------------------|
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.3666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  16855  Z= 0.129
  Angle     :  0.609  10.503  23994  Z= 0.346
  Chirality :  0.041   0.199   2723
  Planarity :  0.004   0.043   2047
  Dihedral  : 29.109  87.766   4498
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.65 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 21.21 %
    Favored  : 76.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.73 (0.24), residues: 1247
  helix:  2.12 (0.18), residues: 808
  sheet:  0.60 (0.68), residues: 73
  loop : -0.98 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG K 450 
 TYR   0.025   0.001   TYR D  87 
 PHE   0.012   0.001   PHE K 706 
 TRP   0.008   0.001   TRP K 316 
 HIS   0.003   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00234 /  0.13 (16855)
  covalent geometry    : angle       0.60909 /  0.35 (23994)
  hydrogen bonds       : bond        0.04322 /  2.88 (  973)
  hydrogen bonds       : angle       3.54141 /  2.55 ( 2515)

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

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

  2494 Ramachandran restraints generated.
    1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2494 Ramachandran restraints generated.
    1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 149
  time to evaluate  : 0.493 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 ARG cc_start: 0.8610 (ttt-90) cc_final: 0.8310 (tmt-80)
REVERT: B   77 LYS cc_start: 0.9036 (mmtp) cc_final: 0.8758 (mttm)
REVERT: C   56 GLU cc_start: 0.8487 (tt0) cc_final: 0.7904 (tt0)
REVERT: D   60 GLN cc_start: 0.8699 (tm-30) cc_final: 0.8382 (tm-30)
REVERT: D   63 MET cc_start: 0.9096 (tpp) cc_final: 0.8782 (tpp)
REVERT: D  117 GLU cc_start: 0.8543 (tp30) cc_final: 0.8209 (tm-30)
REVERT: E   60 GLU cc_start: 0.7207 (pm20) cc_final: 0.6871 (pm20)
REVERT: G   75 LYS cc_start: 0.9058 (mtpp) cc_final: 0.8636 (mtpp)
REVERT: G   94 ASN cc_start: 0.9050 (t0) cc_final: 0.8708 (t0)
REVERT: H  117 GLU cc_start: 0.8033 (tt0) cc_final: 0.7430 (tm-30)
REVERT: K  306 ASP cc_start: 0.6996 (OUTLIER) cc_final: 0.6763 (t0)
REVERT: K  331 MET cc_start: 0.7107 (tpp) cc_final: 0.6521 (tpp)
REVERT: K  447 VAL cc_start: 0.6534 (t) cc_final: 0.6283 (t)
REVERT: K  557 ASP cc_start: 0.8226 (m-30) cc_final: 0.7899 (p0)
REVERT: K  709 MET cc_start: 0.5838 (mpp) cc_final: 0.5552 (mpp)
  outliers start: 27
  outliers final: 22
  residues processed: 167
  average time/residue: 0.1314
  time to fit residues: 32.0233
Evaluate side-chains
  166 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 143
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   60 GLU
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   99 HIS
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain E residue  125 ILE
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain K residue  306 ASP
Chi-restraints excluded: chain K residue  357 ILE
Chi-restraints excluded: chain K residue  363 THR
Chi-restraints excluded: chain K residue  486 LEU
Chi-restraints excluded: chain K residue  494 LEU
Chi-restraints excluded: chain K residue  503 LEU
Chi-restraints excluded: chain K residue  521 LEU
Chi-restraints excluded: chain K residue  570 ASP
Chi-restraints excluded: chain K residue  681 LEU
Chi-restraints excluded: chain K residue  691 LEU
Chi-restraints excluded: chain K residue  769 ARG
Chi-restraints excluded: chain K residue  792 ILE
Chi-restraints excluded: chain K residue  804 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 138 optimal weight:   10.0000
   chunk 44 optimal weight:    4.9990
   chunk 98 optimal weight:   50.0000
   chunk 103 optimal weight:    6.9990
   chunk 150 optimal weight:    1.9990
   chunk 72 optimal weight:   50.0000
   chunk 26 optimal weight:    4.9990
   chunk 148 optimal weight:    6.9990
   chunk 149 optimal weight:    7.9990
   chunk 118 optimal weight:   20.0000
   overall best weight:    3.9988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E  69 GLN
F  25 ASN
K 676 GLN
** K 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 767 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.106230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.066196 restraints weight = 50078.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.068184 restraints weight = 24183.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.069479 restraints weight = 16174.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.070149 restraints weight = 13129.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.070505 restraints weight = 11888.685|
|-----------------------------------------------------------------------------|
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.3859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  16855  Z= 0.241
  Angle     :  0.708  11.189  23994  Z= 0.386
  Chirality :  0.045   0.239   2723
  Planarity :  0.005   0.043   2047
  Dihedral  : 29.315  87.591   4498
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.61 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 22.12 %
    Favored  : 75.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.34 (0.24), residues: 1247
  helix:  1.84 (0.18), residues: 807
  sheet:  0.62 (0.67), residues: 72
  loop : -1.23 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG K 450 
 TYR   0.032   0.002   TYR D  87 
 PHE   0.012   0.001   PHE C  25 
 TRP   0.007   0.001   TRP K 314 
 HIS   0.009   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00525 /  0.24 (16855)
  covalent geometry    : angle       0.70769 /  0.39 (23994)
  hydrogen bonds       : bond        0.05622 /  3.77 (  973)
  hydrogen bonds       : angle       3.89048 /  2.81 ( 2515)

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

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

  2494 Ramachandran restraints generated.
    1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2494 Ramachandran restraints generated.
    1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 134
  time to evaluate  : 0.474 
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: B   43 VAL cc_start: 0.9182 (t) cc_final: 0.8966 (p)
REVERT: C   56 GLU cc_start: 0.8399 (tt0) cc_final: 0.7976 (tt0)
REVERT: D   63 MET cc_start: 0.9123 (tpp) cc_final: 0.8831 (tpp)
REVERT: D  117 GLU cc_start: 0.8535 (tp30) cc_final: 0.8181 (tm-30)
REVERT: E   60 GLU cc_start: 0.7703 (pm20) cc_final: 0.7402 (pm20)
REVERT: G   94 ASN cc_start: 0.9116 (t0) cc_final: 0.8764 (t0)
REVERT: H  117 GLU cc_start: 0.8033 (tt0) cc_final: 0.7736 (tm-30)
REVERT: K  306 ASP cc_start: 0.7016 (OUTLIER) cc_final: 0.6768 (t0)
REVERT: K  447 VAL cc_start: 0.6495 (t) cc_final: 0.6215 (t)
REVERT: K  486 LEU cc_start: 0.6956 (OUTLIER) cc_final: 0.6385 (pp)
REVERT: K  709 MET cc_start: 0.6125 (mpp) cc_final: 0.5809 (mpp)
  outliers start: 23
  outliers final: 19
  residues processed: 151
  average time/residue: 0.1075
  time to fit residues: 24.3726
Evaluate side-chains
  151 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 130
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   99 HIS
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain E residue  125 ILE
Chi-restraints excluded: chain K residue  306 ASP
Chi-restraints excluded: chain K residue  357 ILE
Chi-restraints excluded: chain K residue  363 THR
Chi-restraints excluded: chain K residue  486 LEU
Chi-restraints excluded: chain K residue  494 LEU
Chi-restraints excluded: chain K residue  503 LEU
Chi-restraints excluded: chain K residue  521 LEU
Chi-restraints excluded: chain K residue  681 LEU
Chi-restraints excluded: chain K residue  691 LEU
Chi-restraints excluded: chain K residue  767 GLN
Chi-restraints excluded: chain K residue  769 ARG
Chi-restraints excluded: chain K residue  792 ILE
Chi-restraints excluded: chain K residue  804 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 137 optimal weight:    6.9990
   chunk 70 optimal weight:    0.7980
   chunk 91 optimal weight:   20.0000
   chunk 23 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   chunk 149 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   overall best weight:    0.9586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E  69 GLN
** K 732 ASN ** 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 = 0.3931 r_free = 0.3931 target = 0.106346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.066342 restraints weight = 49954.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.068419 restraints weight = 24013.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.069695 restraints weight = 16023.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.070366 restraints weight = 13024.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.070735 restraints weight = 11800.511|
|-----------------------------------------------------------------------------|
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.3873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.291  16855  Z= 0.266
  Angle     :  0.858  59.200  23994  Z= 0.493
  Chirality :  0.045   0.244   2723
  Planarity :  0.005   0.043   2047
  Dihedral  : 29.320  87.627   4498
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 12.87
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.53 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 22.49 %
    Favored  : 75.50 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.32 (0.24), residues: 1247
  helix:  1.82 (0.18), residues: 807
  sheet:  0.62 (0.67), residues: 72
  loop : -1.23 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG K 450 
 TYR   0.030   0.002   TYR D  87 
 PHE   0.011   0.001   PHE C  25 
 TRP   0.007   0.001   TRP K 461 
 HIS   0.009   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00560 /  0.27 (16855)
  covalent geometry    : angle       0.85796 /  0.49 (23994)
  hydrogen bonds       : bond        0.05567 /  3.73 (  973)
  hydrogen bonds       : angle       3.88726 /  2.80 ( 2515)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3018.79 seconds
wall clock time: 52 minutes 35.16 seconds (3155.16 seconds total)