Starting phenix.real_space_refine
on Thu Sep 18 07:09:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b2t_44114/09_2025/9b2t_44114.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b2t_44114/09_2025/9b2t_44114.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.99
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b2t_44114/09_2025/9b2t_44114.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b2t_44114/09_2025/9b2t_44114.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b2t_44114/09_2025/9b2t_44114.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b2t_44114/09_2025/9b2t_44114.map"
  }
  resolution = 2.99
  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=   0.017
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     314      5.49       5
     S      27      5.16       5
     C    8588      2.51       5
     N    2815      2.21       5
     O    3450      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 15194
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "I"
      Number of atoms: 3196
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 157, 3196
          Classifications: {'DNA': 157}
          Link IDs: {'rna3p': 156}
    Chain: "J"
      Number of atoms: 3241
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 157, 3241
          Classifications: {'DNA': 157}
          Link IDs: {'rna3p': 156}
    Chain: "A"
      Number of atoms: 811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 811
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 795
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 795
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 5, 'TRANS': 97}
    Chain: "D"
      Number of atoms: 767
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 767
          Classifications: {'peptide': 97}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 94}
    Chain: "E"
      Number of atoms: 817
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 817
          Classifications: {'peptide': 99}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "G"
      Number of atoms: 850
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 850
          Classifications: {'peptide': 110}
          Link IDs: {'PTRANS': 5, 'TRANS': 104}
    Chain: "H"
      Number of atoms: 757
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 757
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 2, 'TRANS': 93}
    Chain: "K"
      Number of atoms: 2636
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 329, 2636
          Classifications: {'peptide': 329}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 316}
  Time building chain proxies: 3.45, per 1000 atoms: 0.23
  Number of scatterers: 15194
  At special positions: 0
  Unit cell: (82.45, 170.72, 134.83, 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      27     16.00
     P     314     15.00
     O    3450      8.00
     N    2815      7.00
     C    8588      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: 1.15
  Conformation dependent library (CDL) restraints added in 431.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2060

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 14 sheets defined
      61.6% alpha, 7.2% beta
      144 base pairs and 279 stacking pairs defined.
    Time for finding SS restraints: 2.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 63 through 76
      removed outlier: 3.683A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.569A  pdb=" N   ALA A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.585A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 4.317A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
      removed outlier: 3.627A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 21
    Processing helix  chain 'C' and resid 27 through 36
    Processing helix  chain 'C' and resid 46 through 73
    Processing helix  chain 'C' and resid 79 through 89
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
      removed outlier: 3.619A  pdb=" N   ASN D  81 " --> pdb=" O   LEU D  77 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 87 through 99
    Processing helix  chain 'D' and resid 100 through 121
      removed outlier: 3.614A  pdb=" N   HIS D 106 " --> pdb=" O   GLU D 102 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 55
    Processing helix  chain 'E' and resid 63 through 76
      removed outlier: 3.810A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.601A  pdb=" N   ALA E 114 " --> pdb=" O   CYS E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 131
      removed outlier: 3.592A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 4.458A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
      removed outlier: 3.597A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 27 through 36
    Processing helix  chain 'G' and resid 46 through 73
    Processing helix  chain 'G' and resid 79 through 89
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
      removed outlier: 3.576A  pdb=" N   ASN H  81 " --> pdb=" O   LEU H  77 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 99
      removed outlier: 3.510A  pdb=" N   ILE H  91 " --> pdb=" O   THR H  87 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 101 through 121
      removed outlier: 3.797A  pdb=" N   LYS H 105 " --> pdb=" O   GLY H 101 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 474 through 479
      removed outlier: 3.799A  pdb=" N   CYS K 478 " --> pdb=" O   PRO K 474 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 481 through 486
      removed outlier: 3.557A  pdb=" N   ARG K 486 " --> pdb=" O   GLU K 482 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 528 through 546
      removed outlier: 3.529A  pdb=" N   ILE K 532 " --> pdb=" O   THR K 528 " (cutoff:3.500A)
      Proline residue:  K 534  - end of helix
      removed outlier: 3.645A  pdb=" N   SER K 546 " --> pdb=" O   LEU K 542 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 570 through 584
    Processing helix  chain 'K' and resid 621 through 644
      removed outlier: 3.752A  pdb=" N   ALA K 625 " --> pdb=" O   SER K 621 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 707 through 712
      removed outlier: 4.287A  pdb=" N   PHE K 711 " --> pdb=" O   ASP K 707 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 716 through 728
      removed outlier: 4.125A  pdb=" N   ASP K 720 " --> pdb=" O   ASP K 716 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 739 through 755
      removed outlier: 3.826A  pdb=" N   LEU K 743 " --> pdb=" O   TYR K 739 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 764 through 781
    Processing helix  chain 'K' and resid 782 through 784
      No H-bonds generated for 'chain 'K' and resid 782 through 784'
    Processing helix  chain 'K' and resid 786 through 794
    Processing helix  chain 'K' and resid 795 through 798
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.904A  pdb=" N   ARG A  83 " --> 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 118 through 119
      removed outlier: 3.560A  pdb=" N   ILE A 119 " --> pdb=" O   ARG B  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.247A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (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
      removed outlier: 6.820A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.888A  pdb=" N   ARG E  83 " --> 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 118 through 119
      removed outlier: 3.513A  pdb=" N   ILE E 119 " --> pdb=" O   ARG F  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.381A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (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
      removed outlier: 3.569A  pdb=" N   ILE G  78 " --> pdb=" O   GLY H  50 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'K' and resid 488 through 492
      removed outlier: 5.357A  pdb=" N   LYS K 489 " --> pdb=" O   GLN K 500 " (cutoff:3.500A)
      removed outlier: 5.599A  pdb=" N   GLN K 500 " --> pdb=" O   LYS K 489 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   LEU K 599 " --> pdb=" O   ILE K 515 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   GLU K 604 " --> pdb=" O   SER K 561 " (cutoff:3.500A)
      removed outlier: 4.540A  pdb=" N   SER K 561 " --> pdb=" O   GLU K 604 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   GLU K 606 " --> pdb=" O   LEU K 559 " (cutoff:3.500A)
      removed outlier: 7.963A  pdb=" N   LEU K 559 " --> pdb=" O   GLU K 606 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'K' and resid 610 through 611
      removed outlier: 3.849A  pdb=" N   ILE K 610 " --> pdb=" O   LEU K 657 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'K' and resid 664 through 669
    Processing sheet with id=AB5, first strand: chain 'K' and resid 693 through 695

    506 hydrogen bonds defined for protein.
    1491 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      376 hydrogen bonds
      752 hydrogen bond angles
      0 basepair planarities
      144 basepair parallelities
      279 stacking parallelities
  Total time for adding SS restraints: 3.62

  Time building geometry restraints manager: 1.45 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 3684
        1.34 -     1.46: 4712
        1.46 -     1.58: 7050
        1.58 -     1.70: 626
        1.70 -     1.82: 44
  Bond restraints: 16116
  Sorted by residual:
  bond pdb=" C3'  DT I -65 "
       pdb=" O3'  DT I -65 "
    ideal  model  delta    sigma   weight residual
    1.422  1.465 -0.043 3.00e-02 1.11e+03 2.01e+00
  bond pdb=" C3'  DT J -17 "
       pdb=" O3'  DT J -17 "
    ideal  model  delta    sigma   weight residual
    1.422  1.458 -0.036 3.00e-02 1.11e+03 1.46e+00
  bond pdb=" CB  LYS K 527 "
       pdb=" CG  LYS K 527 "
    ideal  model  delta    sigma   weight residual
    1.520  1.555 -0.035 3.00e-02 1.11e+03 1.33e+00
  bond pdb=" C3'  DG I -52 "
       pdb=" O3'  DG I -52 "
    ideal  model  delta    sigma   weight residual
    1.422  1.456 -0.034 3.00e-02 1.11e+03 1.32e+00
  bond pdb=" CB  ASP K 611 "
       pdb=" CG  ASP K 611 "
    ideal  model  delta    sigma   weight residual
    1.516  1.545 -0.029 2.50e-02 1.60e+03 1.30e+00
  ... (remaining 16111 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.18: 23052
        3.18 -     6.37: 50
        6.37 -     9.55: 6
        9.55 -    12.73: 1
       12.73 -    15.92: 2
  Bond angle restraints: 23111
  Sorted by residual:
  angle pdb=" CA  LEU K 629 "
        pdb=" CB  LEU K 629 "
        pdb=" CG  LEU K 629 "
      ideal   model   delta    sigma   weight residual
     116.30  132.22  -15.92 3.50e+00 8.16e-02 2.07e+01
  angle pdb=" CA  LEU K 479 "
        pdb=" CB  LEU K 479 "
        pdb=" CG  LEU K 479 "
      ideal   model   delta    sigma   weight residual
     116.30  129.25  -12.95 3.50e+00 8.16e-02 1.37e+01
  angle pdb=" CA  LYS K 527 "
        pdb=" CB  LYS K 527 "
        pdb=" CG  LYS K 527 "
      ideal   model   delta    sigma   weight residual
     114.10  121.18   -7.08 2.00e+00 2.50e-01 1.25e+01
  angle pdb=" CB  MET E  90 "
        pdb=" CG  MET E  90 "
        pdb=" SD  MET E  90 "
      ideal   model   delta    sigma   weight residual
     112.70  123.23  -10.53 3.00e+00 1.11e-01 1.23e+01
  angle pdb=" C   PHE K 499 "
        pdb=" CA  PHE K 499 "
        pdb=" CB  PHE K 499 "
      ideal   model   delta    sigma   weight residual
     109.86  116.07   -6.21 1.80e+00 3.09e-01 1.19e+01
  ... (remaining 23106 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.59: 7297
       35.59 -    71.18: 1567
       71.18 -   106.76: 13
      106.76 -   142.35: 0
      142.35 -   177.94: 4
  Dihedral angle restraints: 8881
    sinusoidal: 5693
      harmonic: 3188
  Sorted by residual:
  dihedral pdb=" CA  ARG K 486 "
           pdb=" C   ARG K 486 "
           pdb=" N   CYS K 487 "
           pdb=" CA  CYS K 487 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.55  -25.45     0      5.00e+00 4.00e-02 2.59e+01
  dihedral pdb=" CA  VAL K 498 "
           pdb=" C   VAL K 498 "
           pdb=" N   PHE K 499 "
           pdb=" CA  PHE K 499 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.05  -24.95     0      5.00e+00 4.00e-02 2.49e+01
  dihedral pdb=" C4'  DT I -65 "
           pdb=" C3'  DT I -65 "
           pdb=" O3'  DT I -65 "
           pdb=" P    DC I -64 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   42.06  177.94     1      3.50e+01 8.16e-04 1.57e+01
  ... (remaining 8878 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 1776
       0.028 -    0.057: 603
       0.057 -    0.085: 155
       0.085 -    0.113: 69
       0.113 -    0.142: 18
  Chirality restraints: 2621
  Sorted by residual:
  chirality pdb=" CA  ILE K 513 "
            pdb=" N   ILE K 513 "
            pdb=" C   ILE K 513 "
            pdb=" CB  ILE K 513 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 5.01e-01
  chirality pdb=" CA  ASN K 730 "
            pdb=" N   ASN K 730 "
            pdb=" C   ASN K 730 "
            pdb=" CB  ASN K 730 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.53e-01
  chirality pdb=" CG  LEU K 573 "
            pdb=" CB  LEU K 573 "
            pdb=" CD1 LEU K 573 "
            pdb=" CD2 LEU K 573 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.46   -0.13 2.00e-01 2.50e+01 3.99e-01
  ... (remaining 2618 not shown)

  Planarity restraints: 1839
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE K 499 "   -0.018 2.00e-02 2.50e+03   1.52e-02 4.06e+00
        pdb=" CG  PHE K 499 "    0.033 2.00e-02 2.50e+03
        pdb=" CD1 PHE K 499 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 PHE K 499 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE K 499 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE K 499 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  PHE K 499 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP B  24 "    0.009 2.00e-02 2.50e+03   1.92e-02 3.70e+00
        pdb=" CG  ASP B  24 "   -0.033 2.00e-02 2.50e+03
        pdb=" OD1 ASP B  24 "    0.012 2.00e-02 2.50e+03
        pdb=" OD2 ASP B  24 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU H 110 "    0.009 2.00e-02 2.50e+03   1.79e-02 3.22e+00
        pdb=" C   GLU H 110 "   -0.031 2.00e-02 2.50e+03
        pdb=" O   GLU H 110 "    0.012 2.00e-02 2.50e+03
        pdb=" N   GLY H 111 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1836 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 460
        2.68 -     3.24: 12573
        3.24 -     3.79: 25907
        3.79 -     4.35: 34045
        4.35 -     4.90: 49667
  Nonbonded interactions: 122652
  Sorted by model distance:
  nonbonded pdb=" O   ASN G  73 "
            pdb=" ND2 ASN G  73 "
     model   vdw
     2.131 3.120
  nonbonded pdb=" OP2  DG I -58 "
            pdb=" OG1 THR K 757 "
     model   vdw
     2.164 3.040
  nonbonded pdb=" O   THR G  76 "
            pdb=" OG1 THR G  76 "
     model   vdw
     2.183 3.040
  nonbonded pdb=" N   GLU E  59 "
            pdb=" OE1 GLU E  59 "
     model   vdw
     2.313 3.120
  nonbonded pdb=" OE1 GLU E  73 "
            pdb=" ND2 ASN F  25 "
     model   vdw
     2.320 3.120
  ... (remaining 122647 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'
  selection = (chain 'E' and resid 37 through 134)
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 16 through 118)
}
ncs_group {
  reference = (chain 'D' and resid 26 through 121)
  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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.070
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.020
  Process input model:                     16.480
  Find NCS groups from input model:        0.130
  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:             0.010
  Load rotamer database and sin/cos tables:6.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8562
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      :  0.004   0.043  16116  Z= 0.169
  Angle     :  0.583  15.917  23111  Z= 0.334
  Chirality :  0.034   0.142   2621
  Planarity :  0.004   0.039   1839
  Dihedral  : 27.107 177.939   6821
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 30.06 %
    Favored  : 67.70 %
  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 aren not related in a simple way.
  whole:  1.58 (0.26), residues: 1080
  helix:  2.46 (0.21), residues: 632
  sheet:  0.01 (0.66), residues: 52
  loop : -1.23 (0.28), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG H  30 
 TYR   0.009   0.001   TYR F  51 
 PHE   0.033   0.002   PHE K 499 
 TRP   0.012   0.001   TRP K 652 
 HIS   0.002   0.001   HIS K 630 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 (16116)
  covalent geometry    : angle       0.58348 (23111)
  hydrogen bonds       : bond        0.12002 (  882)
  hydrogen bonds       : angle       4.08918 ( 2243)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 144
  time to evaluate  : 0.465 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  500 GLN cc_start: 0.8226 (mm110) cc_final: 0.7721 (mm110)
  outliers start: 21
  outliers final: 19
  residues processed: 163
  average time/residue: 0.7468
  time to fit residues: 131.6529
Evaluate side-chains
  161 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 142
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain F residue   21 VAL
Chi-restraints excluded: chain F residue   85 ASP
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  113 SER
Chi-restraints excluded: chain H residue  109 SER
Chi-restraints excluded: chain H residue  120 SER
Chi-restraints excluded: chain K residue  651 HIS
Chi-restraints excluded: chain K residue  656 LEU
Chi-restraints excluded: chain K residue  683 VAL
Chi-restraints excluded: chain K residue  685 ILE
Chi-restraints excluded: chain K residue  742 VAL
Chi-restraints excluded: chain K residue  764 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 98 optimal weight:    0.6980
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:    9.9990
   chunk 103 optimal weight:    0.7980
   chunk 77 optimal weight:    0.9980
   chunk 122 optimal weight:    0.0060
   chunk 91 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.6998

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

Flipped N/Q/H residues before XYZ refinement:
F  27 GLN
K 783 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.129790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.091073 restraints weight = 27643.125|
|-----------------------------------------------------------------------------|
r_work (start): 0.3345 rms_B_bonded: 2.01
r_work: 0.3044 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2903 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8701
moved from start:          0.0695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  16116  Z= 0.157
  Angle     :  0.534  10.863  23111  Z= 0.314
  Chirality :  0.034   0.205   2621
  Planarity :  0.004   0.040   1839
  Dihedral  : 29.020 179.722   4659
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 26.23 %
    Favored  : 69.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.77 (0.26), residues: 1080
  helix:  2.66 (0.21), residues: 643
  sheet:  0.11 (0.67), residues: 42
  loop : -1.37 (0.27), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG K 648 
 TYR   0.007   0.001   TYR F  51 
 PHE   0.018   0.001   PHE K 499 
 TRP   0.010   0.001   TRP K 652 
 HIS   0.004   0.001   HIS K 794 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 (16116)
  covalent geometry    : angle       0.53419 (23111)
  hydrogen bonds       : bond        0.05363 (  882)
  hydrogen bonds       : angle       3.24719 ( 2243)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 149
  time to evaluate  : 0.448 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   73 ASN cc_start: 0.7988 (t0) cc_final: 0.7765 (t160)
REVERT: K  499 PHE cc_start: 0.7897 (OUTLIER) cc_final: 0.7458 (t80)
  outliers start: 36
  outliers final: 12
  residues processed: 172
  average time/residue: 0.7113
  time to fit residues: 132.6751
Evaluate side-chains
  152 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 139
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain E residue   56 LYS
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain F residue   21 VAL
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain H residue  120 SER
Chi-restraints excluded: chain K residue  499 PHE
Chi-restraints excluded: chain K residue  602 VAL
Chi-restraints excluded: chain K residue  605 PHE
Chi-restraints excluded: chain K residue  612 LEU
Chi-restraints excluded: chain K residue  656 LEU
Chi-restraints excluded: chain K residue  683 VAL
Chi-restraints excluded: chain K residue  742 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 4 optimal weight:    4.9990
   chunk 74 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 79 optimal weight:    2.9990
   chunk 111 optimal weight:    0.0170
   chunk 67 optimal weight:    0.8980
   chunk 1 optimal weight:    5.9990
   chunk 73 optimal weight:    0.6980
   chunk 59 optimal weight:    0.4980
   chunk 118 optimal weight:    6.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    0.6018

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

Flipped N/Q/H residues before XYZ refinement:
K 670 ASN
K 737 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.130357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.091694 restraints weight = 27846.862|
|-----------------------------------------------------------------------------|
r_work (start): 0.3358 rms_B_bonded: 1.92
r_work: 0.3065 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2920 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8695
moved from start:          0.0905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  16116  Z= 0.149
  Angle     :  0.531  11.706  23111  Z= 0.309
  Chirality :  0.034   0.161   2621
  Planarity :  0.004   0.040   1839
  Dihedral  : 29.069 179.912   4639
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 27.29 %
    Favored  : 69.83 %
  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 aren not related in a simple way.
  whole:  1.91 (0.26), residues: 1080
  helix:  2.78 (0.21), residues: 644
  sheet:  0.13 (0.65), residues: 47
  loop : -1.35 (0.27), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  30 
 TYR   0.007   0.001   TYR F  51 
 PHE   0.018   0.001   PHE K 499 
 TRP   0.009   0.001   TRP K 652 
 HIS   0.006   0.001   HIS K 630 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (16116)
  covalent geometry    : angle       0.53062 (23111)
  hydrogen bonds       : bond        0.05015 (  882)
  hydrogen bonds       : angle       3.13202 ( 2243)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 145
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8129 (pm20)
REVERT: F   93 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8209 (tt0)
REVERT: G   73 ASN cc_start: 0.7849 (t0) cc_final: 0.7604 (t160)
REVERT: K  499 PHE cc_start: 0.7751 (OUTLIER) cc_final: 0.7330 (t80)
REVERT: K  513 ILE cc_start: 0.8337 (pp) cc_final: 0.7556 (mp)
  outliers start: 27
  outliers final: 16
  residues processed: 158
  average time/residue: 0.7357
  time to fit residues: 125.6530
Evaluate side-chains
  157 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 138
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain D residue   68 GLU
Chi-restraints excluded: chain E residue   56 LYS
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain H residue   29 THR
Chi-restraints excluded: chain H residue   84 SER
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain H residue  120 SER
Chi-restraints excluded: chain K residue  499 PHE
Chi-restraints excluded: chain K residue  545 LEU
Chi-restraints excluded: chain K residue  602 VAL
Chi-restraints excluded: chain K residue  605 PHE
Chi-restraints excluded: chain K residue  656 LEU
Chi-restraints excluded: chain K residue  683 VAL
Chi-restraints excluded: chain K residue  684 SER
Chi-restraints excluded: chain K residue  685 ILE
Chi-restraints excluded: chain K residue  742 VAL
Chi-restraints excluded: chain K residue  764 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 31 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   chunk 126 optimal weight:    7.9990
   chunk 117 optimal weight:    9.9990
   chunk 42 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 54 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9990
   chunk 71 optimal weight:    0.8980
   chunk 83 optimal weight:    4.9990
   chunk 78 optimal weight:    1.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
K 783 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.127959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 78)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.082980 restraints weight = 27556.099|
|-----------------------------------------------------------------------------|
r_work (start): 0.3230 rms_B_bonded: 1.98
r_work: 0.3042 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2906 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.2906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8742
moved from start:          0.1144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  16116  Z= 0.185
  Angle     :  0.543  10.730  23111  Z= 0.319
  Chirality :  0.035   0.144   2621
  Planarity :  0.004   0.039   1839
  Dihedral  : 29.167 177.917   4637
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 26.12 %
    Favored  : 70.04 %
  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 aren not related in a simple way.
  whole:  1.87 (0.26), residues: 1080
  helix:  2.75 (0.21), residues: 642
  sheet:  0.26 (0.59), residues: 57
  loop : -1.39 (0.27), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG K 648 
 TYR   0.011   0.001   TYR F  51 
 PHE   0.013   0.001   PHE K 499 
 TRP   0.008   0.001   TRP K 652 
 HIS   0.006   0.001   HIS K 630 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 (16116)
  covalent geometry    : angle       0.54326 (23111)
  hydrogen bonds       : bond        0.06096 (  882)
  hydrogen bonds       : angle       3.18349 ( 2243)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 134
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8131 (pm20)
REVERT: F   93 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8320 (tt0)
REVERT: G   73 ASN cc_start: 0.8142 (t0) cc_final: 0.7912 (t160)
REVERT: K  499 PHE cc_start: 0.7749 (OUTLIER) cc_final: 0.7306 (t80)
REVERT: K  513 ILE cc_start: 0.8378 (pp) cc_final: 0.7718 (mp)
  outliers start: 36
  outliers final: 18
  residues processed: 158
  average time/residue: 0.7977
  time to fit residues: 135.9601
Evaluate side-chains
  153 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 132
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain D residue   68 GLU
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain E residue   56 LYS
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain F residue   21 VAL
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain H residue   29 THR
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain H residue  120 SER
Chi-restraints excluded: chain K residue  499 PHE
Chi-restraints excluded: chain K residue  545 LEU
Chi-restraints excluded: chain K residue  602 VAL
Chi-restraints excluded: chain K residue  605 PHE
Chi-restraints excluded: chain K residue  656 LEU
Chi-restraints excluded: chain K residue  683 VAL
Chi-restraints excluded: chain K residue  685 ILE
Chi-restraints excluded: chain K residue  742 VAL
Chi-restraints excluded: chain K residue  764 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 55 optimal weight:    3.9990
   chunk 29 optimal weight:    5.9990
   chunk 107 optimal weight:    0.8980
   chunk 119 optimal weight:    4.9990
   chunk 13 optimal weight:    4.9990
   chunk 70 optimal weight:    1.9990
   chunk 63 optimal weight:    3.9990
   chunk 113 optimal weight:    0.0570
   chunk 132 optimal weight:    8.9990
   chunk 43 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9990
   overall best weight:    1.3904

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

Flipped N/Q/H residues before XYZ refinement:
K 598 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.132698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.086854 restraints weight = 29431.489|
|-----------------------------------------------------------------------------|
r_work (start): 0.3215 rms_B_bonded: 1.97
r_work: 0.3022 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2886 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8762
moved from start:          0.1326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  16116  Z= 0.204
  Angle     :  0.567  11.830  23111  Z= 0.328
  Chirality :  0.036   0.142   2621
  Planarity :  0.004   0.043   1839
  Dihedral  : 29.179 177.132   4637
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 24.84 %
    Favored  : 71.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.70 (0.26), residues: 1080
  helix:  2.60 (0.21), residues: 644
  sheet:  0.42 (0.59), residues: 57
  loop : -1.50 (0.27), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  30 
 TYR   0.010   0.001   TYR F  51 
 PHE   0.021   0.002   PHE K 645 
 TRP   0.011   0.001   TRP K 652 
 HIS   0.005   0.001   HIS K 630 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 (16116)
  covalent geometry    : angle       0.56694 (23111)
  hydrogen bonds       : bond        0.06379 (  882)
  hydrogen bonds       : angle       3.18900 ( 2243)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 136
  time to evaluate  : 0.439 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   93 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8329 (tt0)
  outliers start: 39
  outliers final: 24
  residues processed: 160
  average time/residue: 0.7251
  time to fit residues: 125.4858
Evaluate side-chains
  158 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 133
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain D residue   68 GLU
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain E residue   56 LYS
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain F residue   21 VAL
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain H residue   29 THR
Chi-restraints excluded: chain H residue   84 SER
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain K residue  499 PHE
Chi-restraints excluded: chain K residue  545 LEU
Chi-restraints excluded: chain K residue  596 ASP
Chi-restraints excluded: chain K residue  602 VAL
Chi-restraints excluded: chain K residue  605 PHE
Chi-restraints excluded: chain K residue  656 LEU
Chi-restraints excluded: chain K residue  683 VAL
Chi-restraints excluded: chain K residue  685 ILE
Chi-restraints excluded: chain K residue  686 ILE
Chi-restraints excluded: chain K residue  742 VAL
Chi-restraints excluded: chain K residue  748 LEU
Chi-restraints excluded: chain K residue  764 THR
Chi-restraints excluded: chain K residue  788 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 66 optimal weight:    0.7980
   chunk 82 optimal weight:    0.7980
   chunk 98 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9990
   chunk 85 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 133 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 42 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
K 783 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.128186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.089287 restraints weight = 27478.724|
|-----------------------------------------------------------------------------|
r_work (start): 0.3304 rms_B_bonded: 1.71
r_work: 0.3002 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2859 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.2859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8722
moved from start:          0.1391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  16116  Z= 0.163
  Angle     :  0.553  12.261  23111  Z= 0.321
  Chirality :  0.035   0.184   2621
  Planarity :  0.004   0.043   1839
  Dihedral  : 29.156 178.419   4636
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 25.16 %
    Favored  : 71.22 %
  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 aren not related in a simple way.
  whole:  1.80 (0.26), residues: 1080
  helix:  2.68 (0.21), residues: 644
  sheet:  0.36 (0.59), residues: 57
  loop : -1.44 (0.27), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  30 
 TYR   0.012   0.001   TYR F  51 
 PHE   0.015   0.001   PHE K 499 
 TRP   0.009   0.001   TRP K 652 
 HIS   0.006   0.001   HIS K 630 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 (16116)
  covalent geometry    : angle       0.55335 (23111)
  hydrogen bonds       : bond        0.05762 (  882)
  hydrogen bonds       : angle       3.12778 ( 2243)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 137
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   93 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8323 (tt0)
REVERT: K  513 ILE cc_start: 0.8098 (pp) cc_final: 0.7124 (mp)
  outliers start: 34
  outliers final: 20
  residues processed: 154
  average time/residue: 0.7502
  time to fit residues: 124.7407
Evaluate side-chains
  151 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 130
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain D residue   68 GLU
Chi-restraints excluded: chain E residue   56 LYS
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain F residue   21 VAL
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain H residue   29 THR
Chi-restraints excluded: chain H residue   84 SER
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain K residue  499 PHE
Chi-restraints excluded: chain K residue  545 LEU
Chi-restraints excluded: chain K residue  596 ASP
Chi-restraints excluded: chain K residue  602 VAL
Chi-restraints excluded: chain K residue  605 PHE
Chi-restraints excluded: chain K residue  651 HIS
Chi-restraints excluded: chain K residue  683 VAL
Chi-restraints excluded: chain K residue  685 ILE
Chi-restraints excluded: chain K residue  686 ILE
Chi-restraints excluded: chain K residue  742 VAL
Chi-restraints excluded: chain K residue  748 LEU
Chi-restraints excluded: chain K residue  764 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 75 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 93 optimal weight:    0.7980
   chunk 101 optimal weight:    2.9990
   chunk 134 optimal weight:    7.9990
   chunk 18 optimal weight:    3.9990
   chunk 76 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 118 optimal weight:    0.9990
   chunk 17 optimal weight:    3.9990
   chunk 98 optimal weight:    0.6980
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
G  73 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.126007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.085610 restraints weight = 26945.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 1.86
r_work: 0.2952 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2807 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.2807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8766
moved from start:          0.1527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  16116  Z= 0.196
  Angle     :  0.576  11.868  23111  Z= 0.333
  Chirality :  0.036   0.162   2621
  Planarity :  0.004   0.044   1839
  Dihedral  : 29.206 176.502   4634
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 25.27 %
    Favored  : 71.22 %
  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 aren not related in a simple way.
  whole:  1.70 (0.26), residues: 1080
  helix:  2.62 (0.21), residues: 644
  sheet:  0.36 (0.59), residues: 57
  loop : -1.53 (0.27), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  30 
 TYR   0.008   0.001   TYR F  51 
 PHE   0.013   0.002   PHE K 499 
 TRP   0.013   0.001   TRP K 652 
 HIS   0.004   0.001   HIS K 630 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 (16116)
  covalent geometry    : angle       0.57598 (23111)
  hydrogen bonds       : bond        0.06285 (  882)
  hydrogen bonds       : angle       3.20460 ( 2243)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 140
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  513 ILE cc_start: 0.8204 (pp) cc_final: 0.7312 (mp)
  outliers start: 33
  outliers final: 19
  residues processed: 162
  average time/residue: 0.7343
  time to fit residues: 128.8685
Evaluate side-chains
  149 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 130
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain D residue   68 GLU
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain E residue   56 LYS
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain F residue   21 VAL
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain H residue   29 THR
Chi-restraints excluded: chain H residue   84 SER
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain K residue  499 PHE
Chi-restraints excluded: chain K residue  545 LEU
Chi-restraints excluded: chain K residue  602 VAL
Chi-restraints excluded: chain K residue  683 VAL
Chi-restraints excluded: chain K residue  685 ILE
Chi-restraints excluded: chain K residue  742 VAL
Chi-restraints excluded: chain K residue  748 LEU
Chi-restraints excluded: chain K residue  764 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 31 optimal weight:    0.5980
   chunk 42 optimal weight:    0.7980
   chunk 35 optimal weight:    0.3980
   chunk 56 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 119 optimal weight:    8.9990
   chunk 29 optimal weight:    5.9990
   chunk 110 optimal weight:    0.0670
   chunk 43 optimal weight:    0.8980
   chunk 4 optimal weight:    4.9990
   chunk 90 optimal weight:    1.9990
   overall best weight:    0.5518

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

Flipped N/Q/H residues before XYZ refinement:
G  73 ASN
K 783 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.127307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.086979 restraints weight = 27260.850|
|-----------------------------------------------------------------------------|
r_work (start): 0.3277 rms_B_bonded: 1.87
r_work: 0.2986 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2843 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8737
moved from start:          0.1541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  16116  Z= 0.151
  Angle     :  0.562  11.801  23111  Z= 0.323
  Chirality :  0.035   0.183   2621
  Planarity :  0.004   0.063   1839
  Dihedral  : 29.180 177.928   4634
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 26.33 %
    Favored  : 71.11 %
  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 aren not related in a simple way.
  whole:  1.81 (0.26), residues: 1080
  helix:  2.69 (0.21), residues: 645
  sheet:  0.33 (0.59), residues: 57
  loop : -1.45 (0.27), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  96 
 TYR   0.027   0.001   TYR K 736 
 PHE   0.013   0.001   PHE K 499 
 TRP   0.009   0.001   TRP K 652 
 HIS   0.006   0.001   HIS K 630 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 (16116)
  covalent geometry    : angle       0.56190 (23111)
  hydrogen bonds       : bond        0.05620 (  882)
  hydrogen bonds       : angle       3.12741 ( 2243)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 140
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  513 ILE cc_start: 0.8205 (pp) cc_final: 0.7347 (mp)
  outliers start: 24
  outliers final: 17
  residues processed: 154
  average time/residue: 0.7560
  time to fit residues: 125.9113
Evaluate side-chains
  153 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 136
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain D residue   68 GLU
Chi-restraints excluded: chain E residue   56 LYS
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain F residue   21 VAL
Chi-restraints excluded: chain H residue   29 THR
Chi-restraints excluded: chain K residue  499 PHE
Chi-restraints excluded: chain K residue  545 LEU
Chi-restraints excluded: chain K residue  602 VAL
Chi-restraints excluded: chain K residue  603 LEU
Chi-restraints excluded: chain K residue  651 HIS
Chi-restraints excluded: chain K residue  683 VAL
Chi-restraints excluded: chain K residue  685 ILE
Chi-restraints excluded: chain K residue  742 VAL
Chi-restraints excluded: chain K residue  748 LEU
Chi-restraints excluded: chain K residue  764 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 29 optimal weight:    5.9990
   chunk 50 optimal weight:    0.7980
   chunk 8 optimal weight:    3.9990
   chunk 115 optimal weight:    5.9990
   chunk 62 optimal weight:    3.9990
   chunk 80 optimal weight:    2.9990
   chunk 78 optimal weight:    0.7980
   chunk 76 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    1.0384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.127036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.087061 restraints weight = 27310.835|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 1.85
r_work: 0.2965 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work: 0.2819 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8759
moved from start:          0.1629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  16116  Z= 0.175
  Angle     :  0.560  12.888  23111  Z= 0.324
  Chirality :  0.035   0.164   2621
  Planarity :  0.004   0.054   1839
  Dihedral  : 29.173 177.608   4634
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 26.33 %
    Favored  : 71.43 %
  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 aren not related in a simple way.
  whole:  1.79 (0.26), residues: 1080
  helix:  2.69 (0.21), residues: 645
  sheet:  0.31 (0.59), residues: 57
  loop : -1.48 (0.27), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D  30 
 TYR   0.012   0.001   TYR K 736 
 PHE   0.013   0.001   PHE K 499 
 TRP   0.011   0.001   TRP K 652 
 HIS   0.004   0.001   HIS K 630 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 (16116)
  covalent geometry    : angle       0.56000 (23111)
  hydrogen bonds       : bond        0.05755 (  882)
  hydrogen bonds       : angle       3.11352 ( 2243)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 139
  time to evaluate  : 0.468 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  513 ILE cc_start: 0.8241 (pp) cc_final: 0.7431 (mp)
  outliers start: 21
  outliers final: 16
  residues processed: 151
  average time/residue: 0.7405
  time to fit residues: 121.2053
Evaluate side-chains
  155 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 139
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain D residue   68 GLU
Chi-restraints excluded: chain E residue   56 LYS
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain H residue   29 THR
Chi-restraints excluded: chain K residue  499 PHE
Chi-restraints excluded: chain K residue  545 LEU
Chi-restraints excluded: chain K residue  602 VAL
Chi-restraints excluded: chain K residue  651 HIS
Chi-restraints excluded: chain K residue  683 VAL
Chi-restraints excluded: chain K residue  685 ILE
Chi-restraints excluded: chain K residue  742 VAL
Chi-restraints excluded: chain K residue  748 LEU
Chi-restraints excluded: chain K residue  764 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 38 optimal weight:    0.5980
   chunk 78 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 134 optimal weight:    6.9990
   chunk 69 optimal weight:    0.9990
   chunk 110 optimal weight:    9.9990
   chunk 9 optimal weight:    2.9990
   chunk 112 optimal weight:    7.9990
   chunk 79 optimal weight:    0.7980
   chunk 92 optimal weight:    0.4980
   chunk 18 optimal weight:    3.9990
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
G  73 ASN
K 783 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.127407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.086739 restraints weight = 27368.212|
|-----------------------------------------------------------------------------|
r_work (start): 0.3272 rms_B_bonded: 2.02
r_work: 0.2997 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2853 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8721
moved from start:          0.1662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  16116  Z= 0.161
  Angle     :  0.566  14.867  23111  Z= 0.324
  Chirality :  0.035   0.197   2621
  Planarity :  0.004   0.050   1839
  Dihedral  : 29.168 177.909   4634
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 26.65 %
    Favored  : 71.43 %
  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 aren not related in a simple way.
  whole:  1.79 (0.26), residues: 1080
  helix:  2.68 (0.21), residues: 645
  sheet:  0.28 (0.59), residues: 57
  loop : -1.45 (0.27), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  96 
 TYR   0.011   0.001   TYR K 736 
 PHE   0.013   0.001   PHE K 499 
 TRP   0.010   0.001   TRP K 652 
 HIS   0.004   0.001   HIS K 630 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 (16116)
  covalent geometry    : angle       0.56577 (23111)
  hydrogen bonds       : bond        0.05575 (  882)
  hydrogen bonds       : angle       3.13488 ( 2243)

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 138
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  513 ILE cc_start: 0.8247 (pp) cc_final: 0.7437 (mp)
  outliers start: 18
  outliers final: 17
  residues processed: 149
  average time/residue: 0.7316
  time to fit residues: 118.2245
Evaluate side-chains
  152 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 135
  time to evaluate  : 0.519 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain D residue   68 GLU
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain H residue   29 THR
Chi-restraints excluded: chain K residue  499 PHE
Chi-restraints excluded: chain K residue  545 LEU
Chi-restraints excluded: chain K residue  602 VAL
Chi-restraints excluded: chain K residue  651 HIS
Chi-restraints excluded: chain K residue  683 VAL
Chi-restraints excluded: chain K residue  685 ILE
Chi-restraints excluded: chain K residue  686 ILE
Chi-restraints excluded: chain K residue  742 VAL
Chi-restraints excluded: chain K residue  748 LEU
Chi-restraints excluded: chain K residue  764 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 126 optimal weight:   30.0000
   chunk 119 optimal weight:    9.9990
   chunk 7 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   chunk 109 optimal weight:    9.9990
   chunk 95 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9990
   chunk 114 optimal weight:    7.9990
   chunk 38 optimal weight:    0.8980
   chunk 101 optimal weight:    0.9990
   overall best weight:    1.7788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.124964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.084172 restraints weight = 26985.424|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 1.86
r_work: 0.2921 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2781 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8787
moved from start:          0.1806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  16116  Z= 0.233
  Angle     :  0.595  12.330  23111  Z= 0.344
  Chirality :  0.038   0.304   2621
  Planarity :  0.004   0.050   1839
  Dihedral  : 29.268 176.180   4634
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 26.55 %
    Favored  : 71.11 %
  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 aren not related in a simple way.
  whole:  1.64 (0.26), residues: 1080
  helix:  2.62 (0.21), residues: 636
  sheet:  0.25 (0.59), residues: 57
  loop : -1.56 (0.27), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  96 
 TYR   0.014   0.001   TYR K 736 
 PHE   0.014   0.001   PHE K 499 
 TRP   0.013   0.001   TRP K 652 
 HIS   0.004   0.001   HIS K 630 

Details of bonding type rmsd
  covalent geometry    : bond        0.00529 (16116)
  covalent geometry    : angle       0.59494 (23111)
  hydrogen bonds       : bond        0.06872 (  882)
  hydrogen bonds       : angle       3.26079 ( 2243)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6308.07 seconds
wall clock time: 107 minutes 43.61 seconds (6463.61 seconds total)