Starting phenix.real_space_refine
on Thu Mar  5 06:08:26 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7lyc_23592/03_2026/7lyc_23592.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7lyc_23592/03_2026/7lyc_23592.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.94
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7lyc_23592/03_2026/7lyc_23592.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7lyc_23592/03_2026/7lyc_23592.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7lyc_23592/03_2026/7lyc_23592.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7lyc_23592/03_2026/7lyc_23592.map"
  }
  resolution = 2.94
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.072
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 5925 atoms to isotropic.
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     293      5.49       5
     S      29      5.16       5
     C    8834      2.51       5
     N    2874      2.21       5
     O    3445      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 15475
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "B"
      Number of atoms: 707
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 707
          Classifications: {'peptide': 88}
          Link IDs: {'PTRANS': 1, 'TRANS': 86}
    Chain: "D"
      Number of atoms: 751
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 751
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "E"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          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: "H"
      Number of atoms: 737
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
      Conformer: "B"
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
          bond proxies already assigned to first conformer: 735
    Chain: "I"
      Number of atoms: 2996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 2996
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "J"
      Number of atoms: 3010
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 3010
          Classifications: {'DNA': 146}
          Link IDs: {'rna3p': 145}
    Chain: "K"
      Number of atoms: 639
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 639
          Classifications: {'peptide': 80}
          Link IDs: {'PTRANS': 3, 'TRANS': 76}
    Chain: "N"
      Number of atoms: 2683
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 335, 2663
          Classifications: {'peptide': 335}
          Link IDs: {'PTRANS': 18, 'TRANS': 316}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 335, 2663
          Classifications: {'peptide': 335}
          Link IDs: {'PTRANS': 18, 'TRANS': 316}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 2702
    Chain: "C"
      Number of atoms: 830
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 830
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "G"
      Number of atoms: 830
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 830
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N   LEU K  73 " occ=0.45
      ... (6 atoms not shown)
      pdb=" CD2 LEU K  73 " occ=0.45
    residue:
      pdb=" N  ASER N 452 " occ=0.50
      ... (10 atoms not shown)
      pdb=" OG BSER N 452 " occ=0.50
  Time building chain proxies: 3.26, per 1000 atoms: 0.21
  Number of scatterers: 15475
  At special positions: 0
  Unit cell: (108.926, 117.146, 118.174, 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      29     16.00
     P     293     15.00
     O    3445      8.00
     N    2874      7.00
     C    8834      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
  Links applied
    TRANS
      " SER C  11 " - " SER D 123 "
      " SER G  11 " - " SER H 123 "
  Time building additional restraints: 1.17
  Conformation dependent library (CDL) restraints added in 638.5 milliseconds
  

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2224

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 13 sheets defined
      61.7% alpha, 5.8% beta
      140 base pairs and 263 stacking pairs defined.
    Time for finding SS restraints: 1.76
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 79
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 131
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.677A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 92
      removed outlier: 3.520A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 103 through 123
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 79
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.661A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 92
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.505A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 123
    Processing helix  chain 'K' and resid 22 through 35
    Processing helix  chain 'K' and resid 37 through 39
      No H-bonds generated for 'chain 'K' and resid 37 through 39'
    Processing helix  chain 'K' and resid 56 through 60
    Processing helix  chain 'N' and resid 430 through 439
    Processing helix  chain 'N' and resid 440 through 450
    Processing helix  chain 'N' and resid 463 through 472
    Processing helix  chain 'N' and resid 473 through 483
    Processing helix  chain 'N' and resid 491 through 495
    Processing helix  chain 'N' and resid 496 through 505
    Processing helix  chain 'N' and resid 506 through 516
    Processing helix  chain 'N' and resid 529 through 534
    Processing helix  chain 'N' and resid 536 through 544
    Processing helix  chain 'N' and resid 578 through 593
    Processing helix  chain 'N' and resid 617 through 626
    Processing helix  chain 'N' and resid 633 through 643
      removed outlier: 3.554A  pdb=" N   LYS N 637 " --> pdb=" O   PHE N 633 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 648 through 652
      removed outlier: 3.804A  pdb=" N   GLU N 652 " --> pdb=" O   GLU N 649 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 656 through 666
      removed outlier: 3.915A  pdb=" N   SER N 660 " --> pdb=" O   GLY N 656 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 687 through 698
    Processing helix  chain 'N' and resid 711 through 716
    Processing helix  chain 'N' and resid 760 through 770
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 46 through 73
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 92 through 97
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 36
    Processing helix  chain 'G' and resid 46 through 73
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 92 through 97
    Processing helix  chain 'G' and resid 112 through 116
      removed outlier: 3.527A  pdb=" N   LEU G 116 " --> pdb=" O   ALA G 113 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.943A  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
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.369A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54
      removed outlier: 7.085A  pdb=" N   GLY D  53 " --> pdb=" O   ILE C  78 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'D' and resid 88 through 89
    Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.951A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA8, first strand: chain 'F' and resid 96 through 98
      removed outlier: 6.399A  pdb=" N   THR F  96 " --> pdb=" O   THR C 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'H' and resid 53 through 54
      removed outlier: 7.104A  pdb=" N   GLY H  53 " --> pdb=" O   ILE G  78 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'H' and resid 88 through 89
    Processing sheet with id=AB2, first strand: chain 'K' and resid 12 through 17
      removed outlier: 9.097A  pdb=" N   LEU K  67 " --> pdb=" O   GLN K   2 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   PHE K   4 " --> pdb=" O   LEU K  67 " (cutoff:3.500A)
      removed outlier: 7.443A  pdb=" N   LEU K  69 " --> pdb=" O   PHE K   4 " (cutoff:3.500A)
      removed outlier: 6.341A  pdb=" N   LYS K   6 " --> pdb=" O   LEU K  69 " (cutoff:3.500A)
      removed outlier: 8.203A  pdb=" N   LEU K  71 " --> pdb=" O   LYS K   6 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'N' and resid 595 through 597
      removed outlier: 4.380A  pdb=" N   GLY N 574 " --> pdb=" O   TYR N 597 " (cutoff:3.500A)
      removed outlier: 6.169A  pdb=" N   VAL N 571 " --> pdb=" O   HIS N 606 " (cutoff:3.500A)
      removed outlier: 7.606A  pdb=" N   VAL N 608 " --> pdb=" O   VAL N 571 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   ILE N 573 " --> pdb=" O   VAL N 608 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'N' and resid 701 through 702
      removed outlier: 6.455A  pdb=" N   TYR N 676 " --> pdb=" O   TYR N 736 " (cutoff:3.500A)
      removed outlier: 7.201A  pdb=" N   ILE N 738 " --> pdb=" O   TYR N 676 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   TYR N 678 " --> pdb=" O   ILE N 738 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   GLN N 735 " --> pdb=" O   TRP N 756 " (cutoff:3.500A)
      removed outlier: 7.230A  pdb=" N   ALA N 758 " --> pdb=" O   GLN N 735 " (cutoff:3.500A)
      removed outlier: 5.696A  pdb=" N   ILE N 737 " --> pdb=" O   ALA N 758 " (cutoff:3.500A)

    536 hydrogen bonds defined for protein.
    1559 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      358 hydrogen bonds
      712 hydrogen bond angles
      0 basepair planarities
      140 basepair parallelities
      263 stacking parallelities
  Total time for adding SS restraints: 2.95

  Time building geometry restraints manager: 1.62 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1965
        1.32 -     1.44: 5712
        1.44 -     1.56: 8057
        1.56 -     1.69: 584
        1.69 -     1.81: 45
  Bond restraints: 16363
  Sorted by residual:
  bond pdb=" C   GLU E  50 "
       pdb=" O   GLU E  50 "
    ideal  model  delta    sigma   weight residual
    1.237  1.199  0.038 1.19e-02 7.06e+03 1.00e+01
  bond pdb=" C   ARG E 116 "
       pdb=" O   ARG E 116 "
    ideal  model  delta    sigma   weight residual
    1.234  1.194  0.040 1.28e-02 6.10e+03 9.86e+00
  bond pdb=" C   LYS D 116 "
       pdb=" O   LYS D 116 "
    ideal  model  delta    sigma   weight residual
    1.237  1.200  0.036 1.19e-02 7.06e+03 9.24e+00
  bond pdb=" C   VAL E 117 "
       pdb=" O   VAL E 117 "
    ideal  model  delta    sigma   weight residual
    1.236  1.203  0.034 1.19e-02 7.06e+03 7.95e+00
  bond pdb=" C   GLN A  76 "
       pdb=" N   ASP A  77 "
    ideal  model  delta    sigma   weight residual
    1.335  1.301  0.034 1.34e-02 5.57e+03 6.47e+00
  ... (remaining 16358 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.20: 21764
        1.20 -     2.39: 1390
        2.39 -     3.59: 171
        3.59 -     4.78: 24
        4.78 -     5.98: 11
  Bond angle restraints: 23360
  Sorted by residual:
  angle pdb=" N   ALA A 114 "
        pdb=" CA  ALA A 114 "
        pdb=" C   ALA A 114 "
      ideal   model   delta    sigma   weight residual
     113.15  108.44    4.71 1.19e+00 7.06e-01 1.57e+01
  angle pdb=" N   GLU C  91 "
        pdb=" CA  GLU C  91 "
        pdb=" C   GLU C  91 "
      ideal   model   delta    sigma   weight residual
     111.36  115.33   -3.97 1.09e+00 8.42e-01 1.33e+01
  angle pdb=" N   LEU E  48 "
        pdb=" CA  LEU E  48 "
        pdb=" C   LEU E  48 "
      ideal   model   delta    sigma   weight residual
     111.36  107.58    3.78 1.09e+00 8.42e-01 1.20e+01
  angle pdb=" N   ARG A 116 "
        pdb=" CA  ARG A 116 "
        pdb=" C   ARG A 116 "
      ideal   model   delta    sigma   weight residual
     109.41  104.69    4.72 1.52e+00 4.33e-01 9.64e+00
  angle pdb=" N   GLU A  50 "
        pdb=" CA  GLU A  50 "
        pdb=" C   GLU A  50 "
      ideal   model   delta    sigma   weight residual
     111.28  114.41   -3.13 1.09e+00 8.42e-01 8.24e+00
  ... (remaining 23355 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.16: 7531
       33.16 -    66.31: 1554
       66.31 -    99.47: 38
       99.47 -   132.62: 0
      132.62 -   165.78: 2
  Dihedral angle restraints: 9125
    sinusoidal: 5671
      harmonic: 3454
  Sorted by residual:
  dihedral pdb=" CA  PRO H 103 "
           pdb=" C   PRO H 103 "
           pdb=" N   GLY H 104 "
           pdb=" CA  GLY H 104 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.17  -20.83     0      5.00e+00 4.00e-02 1.74e+01
  dihedral pdb=" C4'  DT J -17 "
           pdb=" C3'  DT J -17 "
           pdb=" O3'  DT J -17 "
           pdb=" P    DT J -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   54.22  165.78     1      3.50e+01 8.16e-04 1.54e+01
  dihedral pdb=" C4'  DG J  20 "
           pdb=" C3'  DG J  20 "
           pdb=" O3'  DG J  20 "
           pdb=" P    DG J  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   66.57  153.43     1      3.50e+01 8.16e-04 1.48e+01
  ... (remaining 9122 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 2311
       0.062 -    0.123: 313
       0.123 -    0.185: 20
       0.185 -    0.247: 0
       0.247 -    0.308: 1
  Chirality restraints: 2645
  Sorted by residual:
  chirality pdb=" CA  GLN A  76 "
            pdb=" N   GLN A  76 "
            pdb=" C   GLN A  76 "
            pdb=" CB  GLN A  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.38e+00
  chirality pdb=" CA  LEU N 625 "
            pdb=" N   LEU N 625 "
            pdb=" C   LEU N 625 "
            pdb=" CB  LEU N 625 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.16 2.00e-01 2.50e+01 6.02e-01
  chirality pdb=" CA  ILE N 573 "
            pdb=" N   ILE N 573 "
            pdb=" C   ILE N 573 "
            pdb=" CB  ILE N 573 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.15e-01
  ... (remaining 2642 not shown)

  Planarity restraints: 1950
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I -52 "    0.011 2.00e-02 2.50e+03   1.36e-02 5.57e+00
        pdb=" N9   DG I -52 "   -0.001 2.00e-02 2.50e+03
        pdb=" C8   DG I -52 "    0.001 2.00e-02 2.50e+03
        pdb=" N7   DG I -52 "   -0.003 2.00e-02 2.50e+03
        pdb=" C5   DG I -52 "   -0.004 2.00e-02 2.50e+03
        pdb=" C6   DG I -52 "   -0.016 2.00e-02 2.50e+03
        pdb=" O6   DG I -52 "    0.018 2.00e-02 2.50e+03
        pdb=" N1   DG I -52 "    0.009 2.00e-02 2.50e+03
        pdb=" C2   DG I -52 "   -0.033 2.00e-02 2.50e+03
        pdb=" N2   DG I -52 "    0.018 2.00e-02 2.50e+03
        pdb=" N3   DG I -52 "   -0.000 2.00e-02 2.50e+03
        pdb=" C4   DG I -52 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D 102 "    0.034 5.00e-02 4.00e+02   5.10e-02 4.16e+00
        pdb=" N   PRO D 103 "   -0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO D 103 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO D 103 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER N 496 "    0.033 5.00e-02 4.00e+02   5.00e-02 4.00e+00
        pdb=" N   PRO N 497 "   -0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO N 497 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO N 497 "    0.028 5.00e-02 4.00e+02
  ... (remaining 1947 not shown)

  Histogram of nonbonded interaction distances:
        1.97 -     2.56: 52
        2.56 -     3.14: 11255
        3.14 -     3.73: 26418
        3.73 -     4.31: 38941
        4.31 -     4.90: 57149
  Nonbonded interactions: 133815
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG N 427 "
            pdb=" OE1 GLU N 429 "
     model   vdw
     1.972 3.120
  nonbonded pdb=" O   ASN N 626 "
            pdb=" OD1 ASN N 626 "
     model   vdw
     2.086 3.040
  nonbonded pdb=" O2   DC I  21 "
            pdb=" N2   DG J -21 "
     model   vdw
     2.179 2.496
  nonbonded pdb=" O   ILE N 624 "
            pdb=" OG  SER N 660 "
     model   vdw
     2.186 3.040
  nonbonded pdb=" ND2 ASN N 524 "
            pdb=" OH  TYR N 533 "
     model   vdw
     2.189 3.120
  ... (remaining 133810 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'
}
ncs_group {
  reference = (chain 'B' and resid 20 through 102)
  selection = (chain 'F' and (resid 20 through 101 or (resid 102 and (name N or name CA or nam \ 
e C or name O ))))
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and (resid 31 through 107 or resid 109 through 123))
  selection = (chain 'H' and (resid 31 through 107 or resid 109 through 123))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.45 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:             1.090
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     15.450
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048  16365  Z= 0.270
  Angle     :  0.648   5.980  23366  Z= 0.396
  Chirality :  0.042   0.308   2645
  Planarity :  0.005   0.051   1948
  Dihedral  : 25.815 165.775   6895
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.69 %
    Favored  : 99.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.02 (0.23), residues: 1172
  helix:  0.47 (0.19), residues: 709
  sheet:  0.08 (0.69), residues: 58
  loop : -0.73 (0.28), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A  53 
 TYR   0.016   0.002   TYR H 121 
 PHE   0.010   0.002   PHE A  78 
 TRP   0.011   0.001   TRP N 629 
 HIS   0.002   0.001   HIS C  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00603 (16363)
  covalent geometry    : angle       0.64741 (23360)
  hydrogen bonds       : bond        0.12087 (  894)
  hydrogen bonds       : angle       4.85023 ( 2271)
  link_TRANS           : bond        0.01096 (    2)
  link_TRANS           : angle       1.61988 (    6)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 GLN cc_start: 0.8406 (pp30) cc_final: 0.7784 (pt0)
REVERT: A  129 ARG cc_start: 0.7873 (tpt-90) cc_final: 0.7258 (ttp-170)
REVERT: B   74 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7442 (mt-10)
REVERT: D   85 LYS cc_start: 0.9010 (mttp) cc_final: 0.8765 (mtmm)
REVERT: D   99 ARG cc_start: 0.8308 (mtt-85) cc_final: 0.7965 (mtt180)
REVERT: H   34 LYS cc_start: 0.8071 (ptmt) cc_final: 0.7119 (mmtm)
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 0.9223
  time to fit residues: 144.0766
Evaluate side-chains
  111 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:   20.0000
   chunk 130 optimal weight:    0.8980
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    9.9990
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    4.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A  55 GLN
A  68 GLN
B  75 HIS
E  68 GLN
E  76 GLN
N 626 ASN
C 104 GLN
G  24 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.198364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.153597 restraints weight = 26687.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.3607 rms_B_bonded: 3.14
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3602
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3602 r_free = 0.3602    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3602 r_free = 0.3602    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3602
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.1008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  16365  Z= 0.183
  Angle     :  0.573   6.446  23366  Z= 0.339
  Chirality :  0.038   0.202   2645
  Planarity :  0.005   0.046   1948
  Dihedral  : 28.919 166.678   4517
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  :  7.87 %
    Favored  : 91.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.99 (0.24), residues: 1172
  helix:  1.40 (0.19), residues: 718
  sheet:  0.06 (0.71), residues: 53
  loop : -0.54 (0.29), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG N 529 
 TYR   0.014   0.001   TYR N 446 
 PHE   0.007   0.001   PHE A  67 
 TRP   0.012   0.001   TRP N 629 
 HIS   0.003   0.001   HIS N 433 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 (16363)
  covalent geometry    : angle       0.57250 (23360)
  hydrogen bonds       : bond        0.04857 (  894)
  hydrogen bonds       : angle       3.36016 ( 2271)
  link_TRANS           : bond        0.00205 (    2)
  link_TRANS           : angle       0.75258 (    6)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 122
  time to evaluate  : 0.469 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 GLN cc_start: 0.8245 (pp30) cc_final: 0.7735 (pt0)
REVERT: B   74 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7350 (mt-10)
REVERT: D   71 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6714 (mp0)
REVERT: D   86 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.6442 (mtp85)
REVERT: D   93 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7482 (mt-10)
REVERT: D   99 ARG cc_start: 0.8252 (mtt-85) cc_final: 0.7930 (mtt180)
REVERT: F   59 LYS cc_start: 0.8292 (mtpp) cc_final: 0.7569 (mtmt)
REVERT: H   34 LYS cc_start: 0.7934 (ptmt) cc_final: 0.6781 (mmtm)
REVERT: H   99 ARG cc_start: 0.8046 (mtt-85) cc_final: 0.7793 (mtt180)
REVERT: N  722 TYR cc_start: 0.8959 (t80) cc_final: 0.8756 (t80)
  outliers start: 8
  outliers final: 3
  residues processed: 125
  average time/residue: 0.9391
  time to fit residues: 125.0376
Evaluate side-chains
  119 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 113
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue   86 ARG
Chi-restraints excluded: chain D residue   93 GLU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain G residue  101 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 78 optimal weight:    6.9990
   chunk 2 optimal weight:    0.4980
   chunk 40 optimal weight:    0.6980
   chunk 101 optimal weight:   10.0000
   chunk 135 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 108 optimal weight:    8.9990
   chunk 42 optimal weight:    2.9990
   chunk 106 optimal weight:    9.9990
   chunk 38 optimal weight:    3.9990
   chunk 30 optimal weight:    0.0050
   overall best weight:    1.2398

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

Flipped N/Q/H residues before XYZ refinement:
N 483 HIS
N 626 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.198915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.159237 restraints weight = 29233.824|
|-----------------------------------------------------------------------------|
r_work (start): 0.3745 rms_B_bonded: 2.62
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3745
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3745 r_free = 0.3745    target_work(ls_wunit_k1) = 0.156         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3745 r_free = 0.3745    target_work(ls_wunit_k1) = 0.156         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3745
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.1246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  16365  Z= 0.173
  Angle     :  0.550   6.480  23366  Z= 0.326
  Chirality :  0.037   0.174   2645
  Planarity :  0.004   0.045   1948
  Dihedral  : 28.844 167.711   4517
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  :  9.15 %
    Favored  : 89.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.38 (0.24), residues: 1172
  helix:  1.73 (0.19), residues: 718
  sheet: -0.14 (0.68), residues: 58
  loop : -0.38 (0.30), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  71 
 TYR   0.012   0.001   TYR N 446 
 PHE   0.006   0.001   PHE E  67 
 TRP   0.010   0.001   TRP N 629 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 (16363)
  covalent geometry    : angle       0.54989 (23360)
  hydrogen bonds       : bond        0.04653 (  894)
  hydrogen bonds       : angle       3.22058 ( 2271)
  link_TRANS           : bond        0.00161 (    2)
  link_TRANS           : angle       0.63176 (    6)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 115
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 GLN cc_start: 0.8282 (pp30) cc_final: 0.7552 (pt0)
REVERT: B   74 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7311 (mt-10)
REVERT: B   91 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8040 (tttp)
REVERT: D   71 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.6854 (mp0)
REVERT: D   86 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.6616 (mtp85)
REVERT: D   99 ARG cc_start: 0.8262 (mtt-85) cc_final: 0.7983 (mtt180)
REVERT: H   34 LYS cc_start: 0.8006 (ptmt) cc_final: 0.7076 (mmtm)
REVERT: H   99 ARG cc_start: 0.8124 (mtt-85) cc_final: 0.7908 (mtt180)
REVERT: N  649 GLU cc_start: 0.4931 (OUTLIER) cc_final: 0.4679 (mt-10)
REVERT: N  722 TYR cc_start: 0.8929 (t80) cc_final: 0.8679 (t80)
  outliers start: 15
  outliers final: 4
  residues processed: 122
  average time/residue: 0.9095
  time to fit residues: 118.2459
Evaluate side-chains
  117 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 109
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   91 LYS
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue   86 ARG
Chi-restraints excluded: chain N residue  649 GLU
Chi-restraints excluded: chain N residue  768 MET
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain G residue  101 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 60 optimal weight:    3.9990
   chunk 66 optimal weight:   20.0000
   chunk 120 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 137 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 62 optimal weight:    5.9990
   chunk 72 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
F  93 GLN
N 483 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.194936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.149403 restraints weight = 25058.093|
|-----------------------------------------------------------------------------|
r_work (start): 0.3556 rms_B_bonded: 3.13
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3557
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3557 r_free = 0.3557    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3557 r_free = 0.3557    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3557
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.1276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.058  16365  Z= 0.280
  Angle     :  0.619   6.951  23366  Z= 0.359
  Chirality :  0.041   0.201   2645
  Planarity :  0.005   0.049   1948
  Dihedral  : 29.105 166.950   4517
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 11.61 %
    Favored  : 86.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.11 (0.24), residues: 1172
  helix:  1.51 (0.19), residues: 718
  sheet: -0.01 (0.71), residues: 53
  loop : -0.50 (0.30), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E  49 
 TYR   0.016   0.002   TYR D 121 
 PHE   0.012   0.002   PHE A  78 
 TRP   0.009   0.001   TRP N 629 
 HIS   0.005   0.001   HIS N 483 

Details of bonding type rmsd
  covalent geometry    : bond        0.00659 (16363)
  covalent geometry    : angle       0.61856 (23360)
  hydrogen bonds       : bond        0.05699 (  894)
  hydrogen bonds       : angle       3.38712 ( 2271)
  link_TRANS           : bond        0.00336 (    2)
  link_TRANS           : angle       0.67974 (    6)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 117
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 GLN cc_start: 0.8473 (pp30) cc_final: 0.7913 (pt0)
REVERT: A   90 MET cc_start: 0.8177 (mmp) cc_final: 0.7942 (mmm)
REVERT: B   74 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7388 (mt-10)
REVERT: B   91 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8037 (tttp)
REVERT: D   71 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6868 (mp0)
REVERT: D   85 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8059 (mtmm)
REVERT: D   93 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.7342 (mp0)
REVERT: D   99 ARG cc_start: 0.8248 (mtt-85) cc_final: 0.7915 (mtt180)
REVERT: H   34 LYS cc_start: 0.7926 (ptmt) cc_final: 0.6801 (mmtm)
REVERT: N  474 LEU cc_start: 0.7550 (mm) cc_final: 0.7107 (mp)
  outliers start: 16
  outliers final: 6
  residues processed: 124
  average time/residue: 0.8542
  time to fit residues: 113.5966
Evaluate side-chains
  125 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 115
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   91 LYS
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue   85 LYS
Chi-restraints excluded: chain D residue   86 ARG
Chi-restraints excluded: chain D residue   93 GLU
Chi-restraints excluded: chain N residue  768 MET
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  101 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 79 optimal weight:   10.0000
   chunk 16 optimal weight:    1.9990
   chunk 90 optimal weight:    9.9990
   chunk 80 optimal weight:    9.9990
   chunk 68 optimal weight:    6.9990
   chunk 34 optimal weight:    0.6980
   chunk 85 optimal weight:    7.9990
   chunk 71 optimal weight:    3.9990
   chunk 129 optimal weight:    0.8980
   chunk 56 optimal weight:    4.9990
   chunk 88 optimal weight:    0.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
N 483 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.196262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.151258 restraints weight = 35020.419|
|-----------------------------------------------------------------------------|
r_work (start): 0.3510 rms_B_bonded: 3.31
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3540
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3540 r_free = 0.3540    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3540 r_free = 0.3540    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3540
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.1307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  16365  Z= 0.204
  Angle     :  0.582   8.769  23366  Z= 0.343
  Chirality :  0.039   0.204   2645
  Planarity :  0.004   0.047   1948
  Dihedral  : 29.073 167.822   4517
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 13.09 %
    Favored  : 85.43 %
  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 are not related in a simple way.
  whole:  1.25 (0.24), residues: 1172
  helix:  1.63 (0.19), residues: 719
  sheet:  0.03 (0.72), residues: 53
  loop : -0.47 (0.30), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  71 
 TYR   0.014   0.002   TYR D 121 
 PHE   0.008   0.001   PHE A  78 
 TRP   0.007   0.001   TRP N 756 
 HIS   0.004   0.001   HIS N 483 

Details of bonding type rmsd
  covalent geometry    : bond        0.00470 (16363)
  covalent geometry    : angle       0.58191 (23360)
  hydrogen bonds       : bond        0.05158 (  894)
  hydrogen bonds       : angle       3.29655 ( 2271)
  link_TRANS           : bond        0.00217 (    2)
  link_TRANS           : angle       0.50860 (    6)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 115
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 GLN cc_start: 0.8372 (pp30) cc_final: 0.7707 (pt0)
REVERT: A   90 MET cc_start: 0.8239 (mmp) cc_final: 0.7996 (mmm)
REVERT: B   74 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7395 (mt-10)
REVERT: B   91 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8047 (tttp)
REVERT: D   71 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.6890 (mp0)
REVERT: D   85 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8016 (mtmm)
REVERT: D   93 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.7353 (mp0)
REVERT: D   99 ARG cc_start: 0.8230 (mtt-85) cc_final: 0.7907 (mtt180)
REVERT: H   34 LYS cc_start: 0.7922 (ptmt) cc_final: 0.6741 (mmtm)
REVERT: N  474 LEU cc_start: 0.7487 (mm) cc_final: 0.7048 (mp)
REVERT: N  519 SER cc_start: 0.7740 (t) cc_final: 0.7407 (p)
  outliers start: 14
  outliers final: 6
  residues processed: 122
  average time/residue: 0.8499
  time to fit residues: 111.0173
Evaluate side-chains
  121 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 111
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   91 LYS
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue   85 LYS
Chi-restraints excluded: chain D residue   86 ARG
Chi-restraints excluded: chain D residue   93 GLU
Chi-restraints excluded: chain N residue  768 MET
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain G residue  101 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 69 optimal weight:    5.9990
   chunk 56 optimal weight:    4.9990
   chunk 119 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 133 optimal weight:    0.9990
   chunk 67 optimal weight:   10.0000
   chunk 111 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
E  76 GLN
N 483 HIS
** N 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.194515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.152073 restraints weight = 28847.770|
|-----------------------------------------------------------------------------|
r_work (start): 0.3655 rms_B_bonded: 2.80
r_work (final): 0.3655
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3655
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3655 r_free = 0.3655    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3655 r_free = 0.3655    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3655
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.1393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.057  16365  Z= 0.279
  Angle     :  0.617   7.974  23366  Z= 0.359
  Chirality :  0.042   0.208   2645
  Planarity :  0.005   0.051   1948
  Dihedral  : 29.133 169.060   4517
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 12.99 %
    Favored  : 85.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.06 (0.24), residues: 1172
  helix:  1.46 (0.19), residues: 720
  sheet: -0.01 (0.72), residues: 53
  loop : -0.53 (0.29), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E  49 
 TYR   0.015   0.002   TYR D 121 
 PHE   0.012   0.002   PHE A  78 
 TRP   0.010   0.001   TRP N 629 
 HIS   0.005   0.001   HIS N 433 

Details of bonding type rmsd
  covalent geometry    : bond        0.00656 (16363)
  covalent geometry    : angle       0.61745 (23360)
  hydrogen bonds       : bond        0.05710 (  894)
  hydrogen bonds       : angle       3.37169 ( 2271)
  link_TRANS           : bond        0.00325 (    2)
  link_TRANS           : angle       0.64184 (    6)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 116
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 GLN cc_start: 0.8417 (pp30) cc_final: 0.7877 (pt0)
REVERT: A   90 MET cc_start: 0.8204 (mmp) cc_final: 0.7928 (mmm)
REVERT: B   74 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7390 (mt-10)
REVERT: B   91 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8101 (tttp)
REVERT: D   71 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.6908 (mp0)
REVERT: D   85 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8032 (mtmm)
REVERT: D   93 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.7404 (mp0)
REVERT: D   99 ARG cc_start: 0.8239 (mtt-85) cc_final: 0.7904 (mtt180)
REVERT: H   34 LYS cc_start: 0.8011 (ptmt) cc_final: 0.6934 (mmtm)
REVERT: N  474 LEU cc_start: 0.7535 (mm) cc_final: 0.7035 (mp)
REVERT: N  519 SER cc_start: 0.7601 (t) cc_final: 0.7328 (p)
  outliers start: 18
  outliers final: 10
  residues processed: 124
  average time/residue: 0.8685
  time to fit residues: 115.3799
Evaluate side-chains
  129 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 115
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   91 LYS
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue   85 LYS
Chi-restraints excluded: chain D residue   86 ARG
Chi-restraints excluded: chain D residue   93 GLU
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain N residue  430 THR
Chi-restraints excluded: chain N residue  690 ASN
Chi-restraints excluded: chain N residue  768 MET
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  101 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 93 optimal weight:    8.9990
   chunk 20 optimal weight:    0.9990
   chunk 97 optimal weight:    5.9990
   chunk 10 optimal weight:    0.8980
   chunk 99 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 26 optimal weight:    6.9990
   chunk 31 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 44 optimal weight:    4.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
E  76 GLN
N 483 HIS
** N 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.197374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.152323 restraints weight = 24765.553|
|-----------------------------------------------------------------------------|
r_work (start): 0.3657 rms_B_bonded: 2.95
r_work (final): 0.3657
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3617
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3617 r_free = 0.3617    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3617 r_free = 0.3617    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3617
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.1428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  16365  Z= 0.171
  Angle     :  0.566   7.414  23366  Z= 0.335
  Chirality :  0.037   0.181   2645
  Planarity :  0.004   0.047   1948
  Dihedral  : 29.059 171.110   4517
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 13.88 %
    Favored  : 84.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.41 (0.24), residues: 1172
  helix:  1.75 (0.19), residues: 719
  sheet:  0.07 (0.73), residues: 53
  loop : -0.39 (0.30), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  71 
 TYR   0.012   0.001   TYR N 676 
 PHE   0.007   0.001   PHE A  67 
 TRP   0.012   0.001   TRP N 629 
 HIS   0.004   0.001   HIS N 483 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 (16363)
  covalent geometry    : angle       0.56556 (23360)
  hydrogen bonds       : bond        0.04832 (  894)
  hydrogen bonds       : angle       3.23544 ( 2271)
  link_TRANS           : bond        0.00157 (    2)
  link_TRANS           : angle       0.47727 (    6)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 115
  time to evaluate  : 0.419 
Fit side-chains
REVERT: A   76 GLN cc_start: 0.8209 (pp30) cc_final: 0.7690 (pt0)
REVERT: A   90 MET cc_start: 0.8167 (mmp) cc_final: 0.7911 (mmm)
REVERT: B   74 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7416 (mt-10)
REVERT: B   91 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8014 (tttp)
REVERT: D   71 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6772 (mp0)
REVERT: D   85 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8133 (mtmm)
REVERT: D   86 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.6703 (mtp85)
REVERT: D   93 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.7309 (mp0)
REVERT: D   99 ARG cc_start: 0.8219 (mtt-85) cc_final: 0.7914 (mtt180)
REVERT: H   34 LYS cc_start: 0.7999 (ptmt) cc_final: 0.6894 (mmtm)
REVERT: N  474 LEU cc_start: 0.7458 (mm) cc_final: 0.6979 (mp)
REVERT: N  519 SER cc_start: 0.7678 (t) cc_final: 0.7344 (p)
  outliers start: 15
  outliers final: 7
  residues processed: 123
  average time/residue: 0.8202
  time to fit residues: 108.4620
Evaluate side-chains
  124 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 112
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   91 LYS
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue   85 LYS
Chi-restraints excluded: chain D residue   86 ARG
Chi-restraints excluded: chain D residue   93 GLU
Chi-restraints excluded: chain N residue  430 THR
Chi-restraints excluded: chain N residue  690 ASN
Chi-restraints excluded: chain N residue  768 MET
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  101 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 112 optimal weight:    0.5980
   chunk 90 optimal weight:    8.9990
   chunk 40 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 129 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 66 optimal weight:   20.0000
   chunk 73 optimal weight:    4.9990
   chunk 0 optimal weight:    6.9990
   chunk 126 optimal weight:    1.9990
   chunk 78 optimal weight:    6.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
E  76 GLN
N 483 HIS
** N 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.197226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.153462 restraints weight = 26457.953|
|-----------------------------------------------------------------------------|
r_work (start): 0.3616 rms_B_bonded: 3.24
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3616
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3616 r_free = 0.3616    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3616 r_free = 0.3616    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3616
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.1516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  16365  Z= 0.200
  Angle     :  0.567   8.719  23366  Z= 0.334
  Chirality :  0.038   0.183   2645
  Planarity :  0.004   0.049   1948
  Dihedral  : 28.946 172.323   4517
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 14.37 %
    Favored  : 84.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.48 (0.24), residues: 1172
  helix:  1.78 (0.19), residues: 719
  sheet:  0.13 (0.74), residues: 53
  loop : -0.33 (0.30), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  71 
 TYR   0.013   0.002   TYR N 676 
 PHE   0.007   0.001   PHE A  78 
 TRP   0.012   0.001   TRP N 629 
 HIS   0.003   0.001   HIS N 483 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 (16363)
  covalent geometry    : angle       0.56687 (23360)
  hydrogen bonds       : bond        0.04881 (  894)
  hydrogen bonds       : angle       3.21410 ( 2271)
  link_TRANS           : bond        0.00184 (    2)
  link_TRANS           : angle       0.55438 (    6)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 112
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 GLN cc_start: 0.8244 (pp30) cc_final: 0.7650 (pt0)
REVERT: A   90 MET cc_start: 0.8124 (mmp) cc_final: 0.7891 (mmm)
REVERT: B   74 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7349 (mt-10)
REVERT: B   91 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8082 (tttp)
REVERT: D   71 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.6894 (mp0)
REVERT: D   85 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8030 (mtmm)
REVERT: D   93 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.7194 (mp0)
REVERT: D   99 ARG cc_start: 0.8237 (mtt-85) cc_final: 0.7938 (mtt180)
REVERT: F   92 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7751 (ttp80)
REVERT: H   34 LYS cc_start: 0.7927 (ptmt) cc_final: 0.6762 (mmtm)
REVERT: N  474 LEU cc_start: 0.7421 (mm) cc_final: 0.6936 (mp)
REVERT: N  519 SER cc_start: 0.7692 (t) cc_final: 0.7297 (p)
REVERT: C   74 LYS cc_start: 0.8590 (mtmm) cc_final: 0.8363 (mtmm)
  outliers start: 14
  outliers final: 9
  residues processed: 119
  average time/residue: 0.8697
  time to fit residues: 110.7903
Evaluate side-chains
  125 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 111
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   91 LYS
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue   85 LYS
Chi-restraints excluded: chain D residue   86 ARG
Chi-restraints excluded: chain D residue   93 GLU
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain N residue  430 THR
Chi-restraints excluded: chain N residue  690 ASN
Chi-restraints excluded: chain N residue  768 MET
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  101 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 56 optimal weight:    4.9990
   chunk 126 optimal weight:    1.9990
   chunk 112 optimal weight:    1.9990
   chunk 133 optimal weight:    0.7980
   chunk 61 optimal weight:    4.9990
   chunk 14 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 50 optimal weight:    0.6980
   chunk 94 optimal weight:    2.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
N 483 HIS
** N 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.197312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.153920 restraints weight = 32777.950|
|-----------------------------------------------------------------------------|
r_work (start): 0.3667 rms_B_bonded: 3.11
r_work (final): 0.3667
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3667
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3667 r_free = 0.3667    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3667 r_free = 0.3667    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3667
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.1515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  16365  Z= 0.189
  Angle     :  0.565   8.075  23366  Z= 0.333
  Chirality :  0.037   0.196   2645
  Planarity :  0.004   0.048   1948
  Dihedral  : 28.945 172.412   4517
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 14.57 %
    Favored  : 83.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.51 (0.24), residues: 1172
  helix:  1.81 (0.19), residues: 719
  sheet:  0.14 (0.74), residues: 53
  loop : -0.32 (0.30), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  71 
 TYR   0.013   0.002   TYR N 676 
 PHE   0.008   0.001   PHE E  67 
 TRP   0.010   0.001   TRP N 629 
 HIS   0.003   0.001   HIS N 483 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 (16363)
  covalent geometry    : angle       0.56453 (23360)
  hydrogen bonds       : bond        0.04827 (  894)
  hydrogen bonds       : angle       3.20367 ( 2271)
  link_TRANS           : bond        0.00164 (    2)
  link_TRANS           : angle       0.56174 (    6)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 111
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 GLN cc_start: 0.8270 (pp30) cc_final: 0.7667 (pt0)
REVERT: A   90 MET cc_start: 0.8115 (mmp) cc_final: 0.7877 (mmm)
REVERT: A  122 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8342 (ptpp)
REVERT: B   74 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7398 (mt-10)
REVERT: B   91 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8084 (tttp)
REVERT: D   71 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.6901 (mp0)
REVERT: D   85 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8036 (mtmm)
REVERT: D   93 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.7117 (mp0)
REVERT: D   99 ARG cc_start: 0.8200 (mtt-85) cc_final: 0.7895 (mtt180)
REVERT: F   92 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7767 (ttp80)
REVERT: H   34 LYS cc_start: 0.7949 (ptmt) cc_final: 0.6850 (mmtm)
REVERT: N  474 LEU cc_start: 0.7428 (mm) cc_final: 0.6939 (mp)
REVERT: N  519 SER cc_start: 0.7566 (t) cc_final: 0.7283 (p)
REVERT: C   74 LYS cc_start: 0.8600 (mtmm) cc_final: 0.8395 (mtmm)
  outliers start: 16
  outliers final: 10
  residues processed: 120
  average time/residue: 0.8496
  time to fit residues: 109.1389
Evaluate side-chains
  127 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 111
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 LYS
Chi-restraints excluded: chain B residue   91 LYS
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue   85 LYS
Chi-restraints excluded: chain D residue   86 ARG
Chi-restraints excluded: chain D residue   93 GLU
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain K residue    7 THR
Chi-restraints excluded: chain N residue  430 THR
Chi-restraints excluded: chain N residue  690 ASN
Chi-restraints excluded: chain N residue  768 MET
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  101 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 59 optimal weight:    3.9990
   chunk 135 optimal weight:    2.9990
   chunk 75 optimal weight:    4.9990
   chunk 0 optimal weight:    7.9990
   chunk 113 optimal weight:    2.9990
   chunk 90 optimal weight:    6.9990
   chunk 2 optimal weight:    1.9990
   chunk 61 optimal weight:    4.9990
   chunk 49 optimal weight:    0.8980
   chunk 107 optimal weight:    6.9990
   chunk 120 optimal weight:    3.9990
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
N 483 HIS
** N 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.194652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.152725 restraints weight = 28778.822|
|-----------------------------------------------------------------------------|
r_work (start): 0.3654 rms_B_bonded: 3.04
r_work (final): 0.3654
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3569
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3569 r_free = 0.3569    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3569 r_free = 0.3569    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3569
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.1504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054  16365  Z= 0.260
  Angle     :  0.603   8.236  23366  Z= 0.352
  Chirality :  0.041   0.198   2645
  Planarity :  0.005   0.049   1948
  Dihedral  : 29.064 172.269   4517
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 14.67 %
    Favored  : 83.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.24 (0.24), residues: 1172
  helix:  1.60 (0.19), residues: 726
  sheet:  0.14 (0.73), residues: 53
  loop : -0.48 (0.30), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C  71 
 TYR   0.015   0.002   TYR N 676 
 PHE   0.012   0.002   PHE A  78 
 TRP   0.008   0.001   TRP N 629 
 HIS   0.004   0.001   HIS N 433 

Details of bonding type rmsd
  covalent geometry    : bond        0.00609 (16363)
  covalent geometry    : angle       0.60316 (23360)
  hydrogen bonds       : bond        0.05496 (  894)
  hydrogen bonds       : angle       3.30308 ( 2271)
  link_TRANS           : bond        0.00282 (    2)
  link_TRANS           : angle       0.63729 (    6)

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 111
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 GLN cc_start: 0.8391 (pp30) cc_final: 0.7850 (pt0)
REVERT: A   90 MET cc_start: 0.8224 (mmp) cc_final: 0.7975 (mmm)
REVERT: A  122 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8277 (ptpp)
REVERT: B   74 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7405 (mt-10)
REVERT: B   91 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8084 (tttp)
REVERT: D   71 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.6896 (mp0)
REVERT: D   85 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8042 (mtmm)
REVERT: D   93 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.7298 (mp0)
REVERT: D   99 ARG cc_start: 0.8221 (mtt-85) cc_final: 0.7902 (mtt180)
REVERT: F   92 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.7738 (ttp80)
REVERT: H   34 LYS cc_start: 0.7975 (ptmt) cc_final: 0.6908 (mmtm)
REVERT: N  474 LEU cc_start: 0.7485 (mm) cc_final: 0.6985 (mp)
REVERT: N  519 SER cc_start: 0.7580 (t) cc_final: 0.7294 (p)
  outliers start: 16
  outliers final: 9
  residues processed: 120
  average time/residue: 0.8802
  time to fit residues: 113.1871
Evaluate side-chains
  126 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 111
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 LYS
Chi-restraints excluded: chain B residue   91 LYS
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue   85 LYS
Chi-restraints excluded: chain D residue   86 ARG
Chi-restraints excluded: chain D residue   93 GLU
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain K residue    7 THR
Chi-restraints excluded: chain N residue  430 THR
Chi-restraints excluded: chain N residue  690 ASN
Chi-restraints excluded: chain N residue  768 MET
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  101 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 134 optimal weight:    0.9990
   chunk 53 optimal weight:   10.0000
   chunk 1 optimal weight:    0.9990
   chunk 54 optimal weight:    5.9990
   chunk 42 optimal weight:    0.8980
   chunk 110 optimal weight:    0.9990
   chunk 88 optimal weight:    2.9990
   chunk 50 optimal weight:    0.5980
   chunk 121 optimal weight:    0.9990
   chunk 71 optimal weight:    3.9990
   chunk 78 optimal weight:    5.9990
   overall best weight:    0.8986

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
** N 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.197185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.149850 restraints weight = 20731.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.3508 rms_B_bonded: 2.46
r_work: 0.3107 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2841
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2841 r_free = 0.2841    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2841 r_free = 0.2841    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2841
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.1526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  16365  Z= 0.162
  Angle     :  0.572   7.905  23366  Z= 0.338
  Chirality :  0.037   0.195   2645
  Planarity :  0.004   0.046   1948
  Dihedral  : 29.060 172.589   4517
  Min Nonbonded Distance : 2.132

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 14.76 %
    Favored  : 83.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.49 (0.24), residues: 1172
  helix:  1.81 (0.19), residues: 725
  sheet:  0.13 (0.74), residues: 53
  loop : -0.40 (0.30), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C  71 
 TYR   0.014   0.002   TYR B  51 
 PHE   0.009   0.001   PHE E  67 
 TRP   0.009   0.001   TRP N 629 
 HIS   0.004   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 (16363)
  covalent geometry    : angle       0.57229 (23360)
  hydrogen bonds       : bond        0.04823 (  894)
  hydrogen bonds       : angle       3.24698 ( 2271)
  link_TRANS           : bond        0.00097 (    2)
  link_TRANS           : angle       0.50374 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3731.84 seconds
wall clock time: 64 minutes 55.77 seconds (3895.77 seconds total)