Starting phenix.real_space_refine
on Fri Jun 13 10:04:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b2t_44114/06_2025/9b2t_44114.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b2t_44114/06_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b2t_44114/06_2025/9b2t_44114.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b2t_44114/06_2025/9b2t_44114.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b2t_44114/06_2025/9b2t_44114.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b2t_44114/06_2025/9b2t_44114.cif"
  }
  resolution = 2.99
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 12.41, per 1000 atoms: 0.82
  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: 4.57
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  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: 10.73
  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: 11.48

  Time building geometry restraints manager: 5.54 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:             216.690
  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:             0.020
  Extract box with map and model:          0.640
  Check model and map are aligned:         0.110
  Set scattering table:                    0.150
  Process input model:                     56.090
  Find NCS groups from input model:        0.370
  Set up NCS constraints:                  0.080
  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:21.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  295.770
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.58 (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
 TRP   0.012   0.001   TRP K 652 
 HIS   0.002   0.001   HIS K 630 
 PHE   0.033   0.002   PHE K 499 
 TYR   0.009   0.001   TYR F  51 
 ARG   0.008   0.000   ARG H  30 

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

*********************** 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  : 2.474 
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: 2.0254
  time to fit residues: 354.7267
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  : 1.298 
-------------------------------------------------------------------------------
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 113 optimal weight:    0.9980
   chunk 102 optimal weight:    0.7980
   chunk 56 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 69 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 105 optimal weight:    8.9990
   chunk 40 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9990
   chunk 78 optimal weight:    1.9990
   chunk 122 optimal weight:    0.2980
   overall best weight:    1.0184

-------------------------------------------------------------------------------
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 = 0.3933 r_free = 0.3933 target = 0.128463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.089454 restraints weight = 27623.790|
|-----------------------------------------------------------------------------|
r_work (start): 0.3318 rms_B_bonded: 2.01
r_work: 0.3005 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.2863 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.2863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8728
moved from start:          0.0777

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= 0.177
  Angle     :  0.548  10.771  23111  Z= 0.321
  Chirality :  0.035   0.159   2621
  Planarity :  0.004   0.042   1839
  Dihedral  : 29.091 178.747   4659
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 25.91 %
    Favored  : 70.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.70 (0.26), residues: 1080
  helix:  2.62 (0.21), residues: 643
  sheet:  0.09 (0.67), residues: 42
  loop : -1.41 (0.27), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP K 652 
 HIS   0.005   0.001   HIS K 630 
 PHE   0.015   0.001   PHE K 499 
 TYR   0.010   0.001   TYR F  51 
 ARG   0.007   0.000   ARG K 648 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05914 (  882)
  hydrogen bonds       : angle       3.27387 ( 2243)
  covalent geometry    : bond        0.00383 (16116)
  covalent geometry    : angle       0.54797 (23111)

*********************** 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
  182 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 148
  time to evaluate  : 1.191 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   73 ASN cc_start: 0.8029 (t0) cc_final: 0.7813 (t0)
REVERT: K  499 PHE cc_start: 0.7857 (OUTLIER) cc_final: 0.7348 (t80)
REVERT: K  513 ILE cc_start: 0.8406 (pp) cc_final: 0.7700 (mp)
  outliers start: 34
  outliers final: 14
  residues processed: 169
  average time/residue: 1.4912
  time to fit residues: 273.7022
Evaluate side-chains
  154 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 139
  time to evaluate  : 1.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 LYS
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  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  742 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 74 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 105 optimal weight:    0.6980
   chunk 77 optimal weight:    1.9990
   chunk 72 optimal weight:    0.8980
   chunk 63 optimal weight:    1.9990
   overall best weight:    1.5186

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.126438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.085856 restraints weight = 27283.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.3250 rms_B_bonded: 1.93
r_work: 0.2953 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2803 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8787
moved from start:          0.1127

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= 0.215
  Angle     :  0.572  11.430  23111  Z= 0.334
  Chirality :  0.037   0.166   2621
  Planarity :  0.004   0.042   1839
  Dihedral  : 29.280 176.767   4639
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 25.16 %
    Favored  : 70.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.61 (0.26), residues: 1080
  helix:  2.55 (0.21), residues: 645
  sheet:  0.27 (0.65), residues: 42
  loop : -1.52 (0.27), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP K 652 
 HIS   0.007   0.001   HIS K 630 
 PHE   0.020   0.002   PHE K 556 
 TYR   0.012   0.001   TYR F  51 
 ARG   0.006   0.000   ARG K 648 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06919 (  882)
  hydrogen bonds       : angle       3.33923 ( 2243)
  covalent geometry    : bond        0.00480 (16116)
  covalent geometry    : angle       0.57152 (23111)

*********************** 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
  173 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 134
  time to evaluate  : 1.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   93 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8368 (tt0)
REVERT: K  499 PHE cc_start: 0.7697 (OUTLIER) cc_final: 0.7263 (t80)
  outliers start: 39
  outliers final: 20
  residues processed: 161
  average time/residue: 1.7074
  time to fit residues: 297.5792
Evaluate side-chains
  159 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 137
  time to evaluate  : 1.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain C residue   76 THR
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   80 THR
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 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  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  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 9 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 57 optimal weight:   10.0000
   chunk 50 optimal weight:    1.9990
   chunk 127 optimal weight:    8.9990
   chunk 121 optimal weight:    3.9990
   chunk 29 optimal weight:    5.9990
   chunk 39 optimal weight:    0.0670
   chunk 119 optimal weight:    5.9990
   chunk 103 optimal weight:   20.0000
   overall best weight:    2.0126

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

Flipped N/Q/H residues before XYZ refinement:
K 598 GLN
K 746 HIS
K 778 HIS
K 783 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.125117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.084523 restraints weight = 27230.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 2.12
r_work: 0.2925 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2780 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.2780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8809
moved from start:          0.1507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056  16116  Z= 0.260
  Angle     :  0.602  11.460  23111  Z= 0.351
  Chirality :  0.039   0.143   2621
  Planarity :  0.004   0.045   1839
  Dihedral  : 29.326 176.941   4639
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 24.09 %
    Favored  : 71.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.26), residues: 1080
  helix:  2.42 (0.21), residues: 644
  sheet:  0.33 (0.66), residues: 47
  loop : -1.64 (0.27), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP K 652 
 HIS   0.005   0.001   HIS K 630 
 PHE   0.014   0.002   PHE K 499 
 TYR   0.010   0.001   TYR F  51 
 ARG   0.006   0.000   ARG D  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07552 (  882)
  hydrogen bonds       : angle       3.38953 ( 2243)
  covalent geometry    : bond        0.00594 (16116)
  covalent geometry    : angle       0.60194 (23111)

*********************** 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
  183 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 140
  time to evaluate  : 1.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8426 (ptmt)
REVERT: K  513 ILE cc_start: 0.8132 (pp) cc_final: 0.7270 (mp)
  outliers start: 43
  outliers final: 22
  residues processed: 170
  average time/residue: 1.6972
  time to fit residues: 311.0646
Evaluate side-chains
  161 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 138
  time to evaluate  : 1.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  122 LYS
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   76 THR
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   80 THR
Chi-restraints excluded: chain F residue   21 VAL
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  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
Chi-restraints excluded: chain K residue  788 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 116 optimal weight:    0.0970
   chunk 114 optimal weight:    2.9990
   chunk 59 optimal weight:    0.8980
   chunk 124 optimal weight:   10.0000
   chunk 22 optimal weight:    2.9990
   chunk 56 optimal weight:    0.2980
   chunk 90 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 125 optimal weight:    6.9990
   chunk 87 optimal weight:    0.8980
   chunk 13 optimal weight:    3.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
K 778 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.135612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.089753 restraints weight = 28806.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.3334 rms_B_bonded: 1.79
r_work: 0.3155 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3024 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8785
moved from start:          0.1455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  16116  Z= 0.158
  Angle     :  0.570  12.486  23111  Z= 0.331
  Chirality :  0.036   0.216   2621
  Planarity :  0.004   0.043   1839
  Dihedral  : 29.254 177.752   4638
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 25.37 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.62 (0.26), residues: 1080
  helix:  2.57 (0.21), residues: 643
  sheet:  0.32 (0.59), residues: 57
  loop : -1.58 (0.27), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP K 652 
 HIS   0.006   0.001   HIS K 630 
 PHE   0.015   0.001   PHE K 499 
 TYR   0.009   0.001   TYR F  51 
 ARG   0.006   0.000   ARG D  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06172 (  882)
  hydrogen bonds       : angle       3.26873 ( 2243)
  covalent geometry    : bond        0.00328 (16116)
  covalent geometry    : angle       0.56995 (23111)

*********************** 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
  174 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 144
  time to evaluate  : 1.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   59 GLU cc_start: 0.8543 (pm20) cc_final: 0.8290 (pm20)
REVERT: G   73 ASN cc_start: 0.8351 (t0) cc_final: 0.8129 (t0)
REVERT: K  513 ILE cc_start: 0.8257 (pp) cc_final: 0.7501 (mp)
REVERT: K  612 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8760 (mt)
  outliers start: 30
  outliers final: 18
  residues processed: 161
  average time/residue: 1.6368
  time to fit residues: 284.5649
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  : 1.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 F residue   21 VAL
Chi-restraints excluded: chain H residue   29 THR
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  612 LEU
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 13 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9980
   chunk 131 optimal weight:    5.9990
   chunk 104 optimal weight:    0.0970
   chunk 118 optimal weight:    0.7980
   chunk 19 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9980
   chunk 111 optimal weight:   10.0000
   chunk 23 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   overall best weight:    1.1780

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

Flipped N/Q/H residues before XYZ refinement:
K 746 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.134958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.088307 restraints weight = 29111.564|
|-----------------------------------------------------------------------------|
r_work (start): 0.3334 rms_B_bonded: 1.87
r_work: 0.3152 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3022 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8799
moved from start:          0.1569

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= 0.187
  Angle     :  0.567  11.882  23111  Z= 0.331
  Chirality :  0.036   0.150   2621
  Planarity :  0.004   0.044   1839
  Dihedral  : 29.238 176.310   4638
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 25.37 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.62 (0.26), residues: 1080
  helix:  2.60 (0.21), residues: 645
  sheet:  0.30 (0.60), residues: 52
  loop : -1.63 (0.27), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP K 652 
 HIS   0.005   0.001   HIS K 630 
 PHE   0.012   0.001   PHE K 499 
 TYR   0.009   0.001   TYR F  51 
 ARG   0.007   0.000   ARG D  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06146 (  882)
  hydrogen bonds       : angle       3.21898 ( 2243)
  covalent geometry    : bond        0.00412 (16116)
  covalent geometry    : angle       0.56681 (23111)

*********************** 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: 30
    poor density    : 141
  time to evaluate  : 1.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   73 ASN cc_start: 0.8337 (t0) cc_final: 0.8117 (t0)
  outliers start: 30
  outliers final: 20
  residues processed: 160
  average time/residue: 1.7096
  time to fit residues: 294.7583
Evaluate side-chains
  157 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 137
  time to evaluate  : 1.286 
-------------------------------------------------------------------------------
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 H residue   29 THR
Chi-restraints excluded: chain H residue   49 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  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  764 THR
Chi-restraints excluded: chain K residue  791 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 65 optimal weight:    0.8980
   chunk 104 optimal weight:    6.9990
   chunk 27 optimal weight:    3.9990
   chunk 57 optimal weight:    5.9990
   chunk 30 optimal weight:    0.7980
   chunk 28 optimal weight:    3.9990
   chunk 2 optimal weight:    4.9990
   chunk 122 optimal weight:    0.0170
   chunk 3 optimal weight:    2.9990
   chunk 121 optimal weight:    3.9990
   chunk 119 optimal weight:    6.9990
   overall best weight:    1.7422

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

Flipped N/Q/H residues before XYZ refinement:
** K 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 783 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.133686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 81)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.086715 restraints weight = 28999.604|
|-----------------------------------------------------------------------------|
r_work (start): 0.3289 rms_B_bonded: 2.04
r_work: 0.3105 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2974 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8827
moved from start:          0.1710

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= 0.235
  Angle     :  0.599  11.892  23111  Z= 0.348
  Chirality :  0.038   0.160   2621
  Planarity :  0.004   0.044   1839
  Dihedral  : 29.312 175.859   4635
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 25.48 %
    Favored  : 71.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.48 (0.26), residues: 1080
  helix:  2.48 (0.21), residues: 646
  sheet:  0.15 (0.61), residues: 52
  loop : -1.67 (0.27), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP K 652 
 HIS   0.006   0.001   HIS K 630 
 PHE   0.021   0.002   PHE K 607 
 TYR   0.010   0.001   TYR F  51 
 ARG   0.007   0.000   ARG D  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06968 (  882)
  hydrogen bonds       : angle       3.35265 ( 2243)
  covalent geometry    : bond        0.00533 (16116)
  covalent geometry    : angle       0.59912 (23111)

*********************** 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
  178 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 148
  time to evaluate  : 1.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   96 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8522 (ttp-170)
REVERT: K  513 ILE cc_start: 0.8067 (pp) cc_final: 0.7300 (mp)
  outliers start: 30
  outliers final: 20
  residues processed: 165
  average time/residue: 1.7912
  time to fit residues: 322.4701
Evaluate side-chains
  168 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 147
  time to evaluate  : 1.605 
-------------------------------------------------------------------------------
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 G residue   19 SER
Chi-restraints excluded: chain H residue   29 THR
Chi-restraints excluded: chain H residue   49 THR
Chi-restraints excluded: chain H residue   84 SER
Chi-restraints excluded: chain H residue   96 ARG
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  650 LEU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 123 optimal weight:    0.9990
   chunk 76 optimal weight:    2.9990
   chunk 93 optimal weight:    3.9990
   chunk 109 optimal weight:    0.4980
   chunk 41 optimal weight:    0.0870
   chunk 70 optimal weight:    0.8980
   chunk 19 optimal weight:    3.9990
   chunk 132 optimal weight:    0.3980
   chunk 55 optimal weight:    0.6980
   chunk 17 optimal weight:    2.9990
   overall best weight:    0.5158

-------------------------------------------------------------------------------
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 = 0.4014 r_free = 0.4014 target = 0.136322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.090888 restraints weight = 28534.641|
|-----------------------------------------------------------------------------|
r_work (start): 0.3353 rms_B_bonded: 1.81
r_work: 0.3175 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3046 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8755
moved from start:          0.1719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  16116  Z= 0.153
  Angle     :  0.570  12.288  23111  Z= 0.328
  Chirality :  0.035   0.181   2621
  Planarity :  0.004   0.064   1839
  Dihedral  : 29.208 178.418   4635
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 26.97 %
    Favored  : 70.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.72 (0.26), residues: 1080
  helix:  2.66 (0.21), residues: 644
  sheet:  0.29 (0.60), residues: 57
  loop : -1.56 (0.27), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP K 652 
 HIS   0.006   0.001   HIS K 794 
 PHE   0.016   0.001   PHE K 607 
 TYR   0.008   0.001   TYR K 736 
 ARG   0.007   0.000   ARG D  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05420 (  882)
  hydrogen bonds       : angle       3.18773 ( 2243)
  covalent geometry    : bond        0.00325 (16116)
  covalent geometry    : angle       0.57006 (23111)

*********************** 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
  170 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 147
  time to evaluate  : 1.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   73 ASN cc_start: 0.8270 (t0) cc_final: 0.8062 (t0)
REVERT: K  513 ILE cc_start: 0.8059 (pp) cc_final: 0.7182 (mp)
  outliers start: 23
  outliers final: 18
  residues processed: 160
  average time/residue: 1.8802
  time to fit residues: 325.9221
Evaluate side-chains
  163 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 145
  time to evaluate  : 1.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain D residue   68 GLU
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 H residue   49 THR
Chi-restraints excluded: chain H residue   84 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  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  705 SER
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 90 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 100 optimal weight:    0.9990
   chunk 104 optimal weight:   20.0000
   chunk 15 optimal weight:    7.9990
   chunk 6 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 110 optimal weight:    0.8980
   chunk 30 optimal weight:    0.6980
   chunk 85 optimal weight:    2.9990
   chunk 116 optimal weight:    0.9990
   overall best weight:    1.1186

-------------------------------------------------------------------------------
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 = 0.3991 r_free = 0.3991 target = 0.134764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.088141 restraints weight = 28648.598|
|-----------------------------------------------------------------------------|
r_work (start): 0.3332 rms_B_bonded: 2.21
r_work: 0.3152 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3027 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8792
moved from start:          0.1765

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= 0.183
  Angle     :  0.582  14.441  23111  Z= 0.334
  Chirality :  0.036   0.178   2621
  Planarity :  0.004   0.056   1839
  Dihedral  : 29.246 176.314   4634
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 26.55 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.66 (0.26), residues: 1080
  helix:  2.61 (0.21), residues: 645
  sheet:  0.19 (0.59), residues: 57
  loop : -1.58 (0.28), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP K 652 
 HIS   0.006   0.001   HIS K 630 
 PHE   0.014   0.002   PHE K 607 
 TYR   0.012   0.001   TYR K 736 
 ARG   0.007   0.000   ARG D  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05959 (  882)
  hydrogen bonds       : angle       3.24437 ( 2243)
  covalent geometry    : bond        0.00403 (16116)
  covalent geometry    : angle       0.58193 (23111)

*********************** 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
  167 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 144
  time to evaluate  : 1.210 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 23
  outliers final: 13
  residues processed: 159
  average time/residue: 1.5807
  time to fit residues: 272.0031
Evaluate side-chains
  156 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 143
  time to evaluate  : 1.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 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 H residue   49 THR
Chi-restraints excluded: chain H residue   84 SER
Chi-restraints excluded: chain K residue  499 PHE
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 50 optimal weight:    0.6980
   chunk 121 optimal weight:    2.9990
   chunk 124 optimal weight:    5.9990
   chunk 17 optimal weight:    3.9990
   chunk 78 optimal weight:    0.8980
   chunk 127 optimal weight:    7.9990
   chunk 66 optimal weight:    0.6980
   chunk 34 optimal weight:    0.7980
   chunk 133 optimal weight:    5.9990
   chunk 2 optimal weight:    4.9990
   chunk 45 optimal weight:    0.3980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.4000 r_free = 0.4000 target = 0.135472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.089746 restraints weight = 28650.234|
|-----------------------------------------------------------------------------|
r_work (start): 0.3337 rms_B_bonded: 1.84
r_work: 0.3157 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3029 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8771
moved from start:          0.1791

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= 0.162
  Angle     :  0.582  13.911  23111  Z= 0.332
  Chirality :  0.035   0.271   2621
  Planarity :  0.004   0.053   1839
  Dihedral  : 29.238 176.701   4634
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 27.51 %
    Favored  : 70.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.26), residues: 1080
  helix:  2.61 (0.21), residues: 646
  sheet:  0.22 (0.59), residues: 57
  loop : -1.55 (0.28), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP K 652 
 HIS   0.011   0.001   HIS K 778 
 PHE   0.013   0.002   PHE K 797 
 TYR   0.014   0.001   TYR K 736 
 ARG   0.007   0.000   ARG D  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05715 (  882)
  hydrogen bonds       : angle       3.24386 ( 2243)
  covalent geometry    : bond        0.00347 (16116)
  covalent geometry    : angle       0.58169 (23111)

********************** 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
  160 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 144
  time to evaluate  : 1.231 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 16
  outliers final: 14
  residues processed: 155
  average time/residue: 1.6202
  time to fit residues: 270.9208
Evaluate side-chains
  155 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 141
  time to evaluate  : 1.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 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 H residue   49 THR
Chi-restraints excluded: chain H residue   84 SER
Chi-restraints excluded: chain K residue  499 PHE
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  705 SER
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 35 optimal weight:    0.4980
   chunk 57 optimal weight:    0.8980
   chunk 54 optimal weight:    0.6980
   chunk 71 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 68 optimal weight:    4.9990
   chunk 75 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 130 optimal weight:    5.9990
   chunk 115 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9990
   overall best weight:    0.8184

-------------------------------------------------------------------------------
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 = 0.4002 r_free = 0.4002 target = 0.135529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.089823 restraints weight = 28613.836|
|-----------------------------------------------------------------------------|
r_work (start): 0.3342 rms_B_bonded: 1.81
r_work: 0.3164 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3042 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8766
moved from start:          0.1785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  16116  Z= 0.165
  Angle     :  0.580  12.889  23111  Z= 0.332
  Chirality :  0.035   0.188   2621
  Planarity :  0.004   0.052   1839
  Dihedral  : 29.229 177.097   4634
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 27.19 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.69 (0.26), residues: 1080
  helix:  2.61 (0.21), residues: 646
  sheet:  0.22 (0.60), residues: 57
  loop : -1.54 (0.28), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP K 652 
 HIS   0.008   0.001   HIS K 778 
 PHE   0.013   0.002   PHE K 499 
 TYR   0.014   0.001   TYR K 736 
 ARG   0.007   0.000   ARG D  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05703 (  882)
  hydrogen bonds       : angle       3.23755 ( 2243)
  covalent geometry    : bond        0.00357 (16116)
  covalent geometry    : angle       0.58024 (23111)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 14130.70 seconds
wall clock time: 245 minutes 14.56 seconds (14714.56 seconds total)