Starting phenix.real_space_refine
on Wed Mar  4 09:26:31 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d2k_27141/03_2026/8d2k_27141.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d2k_27141/03_2026/8d2k_27141.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.43
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d2k_27141/03_2026/8d2k_27141.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d2k_27141/03_2026/8d2k_27141.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8d2k_27141/03_2026/8d2k_27141.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d2k_27141/03_2026/8d2k_27141.map"
  }
  resolution = 2.43
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P     156      5.49       5
     Mg     10      5.21       5
     S      20      5.16       5
     C    6940      2.51       5
     N    2220      2.21       5
     O    2949      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 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: 12295
  Number of models: 1
  Model: ""
    Number of chains: 13
    Chain: "A"
      Number of atoms: 8720
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1105, 8720
          Classifications: {'peptide': 1105}
          Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 59, 'TRANS': 1041}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 2189
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 2189
          Unusual residues: {'GTP': 1}
          Classifications: {'RNA': 101, 'undetermined': 1}
          Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 8, 'rna3p_pur': 47, 'rna3p_pyr': 41}
          Link IDs: {'rna2p': 13, 'rna3p': 87, None: 1}
            Not linked:
              pdbres="GTP B   1 "
              pdbres="  G B   2 "
          Chain breaks: 1
    Chain: "X"
      Number of atoms: 267
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 267
          Classifications: {'DNA': 13}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 12}
    Chain: "T"
      Number of atoms: 481
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 481
          Classifications: {'DNA': 24}
          Modifications used: {'p5*END': 1}
          Link IDs: {'rna3p': 23}
    Chain: "D"
      Number of atoms: 264
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 264
          Classifications: {'DNA': 13}
          Modifications used: {'p5*END': 1}
          Link IDs: {'rna3p': 12}
    Chain: "Y"
      Number of atoms: 64
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 64
          Classifications: {'DNA': 3}
          Link IDs: {'rna3p': 2}
    Chain: "A"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 5
          Unusual residues: {' MG': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
    Chain: "B"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 5
          Unusual residues: {' MG': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
    Chain: "A"
      Number of atoms: 162
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 162, 162
          Classifications: {'water': 162}
          Link IDs: {None: 161}
    Chain: "B"
      Number of atoms: 113
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 113, 113
          Classifications: {'water': 113}
          Link IDs: {None: 112}
    Chain: "X"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}
    Chain: "T"
      Number of atoms: 18
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 18
          Classifications: {'water': 18}
          Link IDs: {None: 17}
    Chain: "D"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 2.27, per 1000 atoms: 0.18
  Number of scatterers: 12295
  At special positions: 0
  Unit cell: (94.05, 106.425, 129.525, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      20     16.00
     P     156     15.00
     Mg     10     11.99
     O    2949      8.00
     N    2220      7.00
     C    6940      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.95
  Conformation dependent library (CDL) restraints added in 365.3 milliseconds
  

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2074

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 9 sheets defined
      50.6% alpha, 9.8% beta
      55 base pairs and 101 stacking pairs defined.
    Time for finding SS restraints: 1.86
  Creating SS restraints...
    Processing helix  chain 'A' and resid 59 through 92
    Processing helix  chain 'A' and resid 104 through 116
    Processing helix  chain 'A' and resid 120 through 138
    Processing helix  chain 'A' and resid 147 through 153
    Processing helix  chain 'A' and resid 158 through 173
    Processing helix  chain 'A' and resid 180 through 192
    Processing helix  chain 'A' and resid 221 through 237
    Processing helix  chain 'A' and resid 239 through 251
    Processing helix  chain 'A' and resid 259 through 263
    Processing helix  chain 'A' and resid 279 through 293
    Processing helix  chain 'A' and resid 306 through 319
    Processing helix  chain 'A' and resid 326 through 333
    Processing helix  chain 'A' and resid 339 through 341
      No H-bonds generated for 'chain 'A' and resid 339 through 341'
    Processing helix  chain 'A' and resid 354 through 359
    Processing helix  chain 'A' and resid 364 through 377
    Processing helix  chain 'A' and resid 381 through 391
    Processing helix  chain 'A' and resid 392 through 406
    Processing helix  chain 'A' and resid 421 through 431
    Processing helix  chain 'A' and resid 441 through 456
    Processing helix  chain 'A' and resid 458 through 468
    Processing helix  chain 'A' and resid 486 through 508
    Processing helix  chain 'A' and resid 524 through 553
    Processing helix  chain 'A' and resid 558 through 571
    Processing helix  chain 'A' and resid 594 through 598
    Processing helix  chain 'A' and resid 602 through 604
      No H-bonds generated for 'chain 'A' and resid 602 through 604'
    Processing helix  chain 'A' and resid 611 through 618
    Processing helix  chain 'A' and resid 621 through 627
    Processing helix  chain 'A' and resid 633 through 643
    Processing helix  chain 'A' and resid 653 through 670
      removed outlier: 3.653A  pdb=" N   ARG A 670 " --> pdb=" O   ALA A 666 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 681 through 703
    Processing helix  chain 'A' and resid 712 through 722
    Processing helix  chain 'A' and resid 725 through 730
    Processing helix  chain 'A' and resid 742 through 747
      removed outlier: 3.809A  pdb=" N   LEU A 745 " --> pdb=" O   THR A 742 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   ASP A 746 " --> pdb=" O   LYS A 743 " (cutoff:3.500A)
      removed outlier: 4.879A  pdb=" N   ARG A 747 " --> pdb=" O   ARG A 744 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 742 through 747'
    Processing helix  chain 'A' and resid 748 through 758
    Processing helix  chain 'A' and resid 761 through 777
    Processing helix  chain 'A' and resid 797 through 807
    Processing helix  chain 'A' and resid 809 through 820
    Processing helix  chain 'A' and resid 856 through 861
    Processing helix  chain 'A' and resid 864 through 876
    Processing helix  chain 'A' and resid 957 through 963
    Processing helix  chain 'A' and resid 981 through 986
    Processing helix  chain 'A' and resid 988 through 997
    Processing helix  chain 'A' and resid 1025 through 1033
      removed outlier: 4.140A  pdb=" N   TYR A1032 " --> pdb=" O   MET A1028 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1057 through 1071
      removed outlier: 3.687A  pdb=" N   ALA A1061 " --> pdb=" O   SER A1057 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   SER A1069 " --> pdb=" O   ARG A1065 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ASP A1070 " --> pdb=" O   THR A1066 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1076 through 1086
    Processing helix  chain 'A' and resid 1094 through 1098
    Processing sheet with id=AA1, first strand: chain 'A' and resid 706 through 711
      removed outlier: 6.914A  pdb=" N   TRP A  13 " --> pdb=" O   SER A 512 " (cutoff:3.500A)
      removed outlier: 8.411A  pdb=" N   VAL A 514 " --> pdb=" O   TRP A  13 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   LEU A  15 " --> pdb=" O   VAL A 514 " (cutoff:3.500A)
      removed outlier: 7.842A  pdb=" N   GLU A 516 " --> pdb=" O   LEU A  15 " (cutoff:3.500A)
      removed outlier: 7.456A  pdb=" N   VAL A  17 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   ILE A  24 " --> pdb=" O   VAL A  43 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   VAL A  43 " --> pdb=" O   ILE A  24 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   LEU A  26 " --> pdb=" O   ALA A  41 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   ALA A  41 " --> pdb=" O   LEU A  26 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   ALA A  28 " --> pdb=" O   ILE A  39 " (cutoff:3.500A)
      removed outlier: 5.051A  pdb=" N   ILE A  39 " --> pdb=" O   ALA A  28 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   SER A  30 " --> pdb=" O   LYS A  37 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ALA A 824 " --> pdb=" O   ALA A  42 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 301 through 304
    Processing sheet with id=AA3, first strand: chain 'A' and resid 588 through 591
    Processing sheet with id=AA4, first strand: chain 'A' and resid 846 through 849
    Processing sheet with id=AA5, first strand: chain 'A' and resid 854 through 855
    Processing sheet with id=AA6, first strand: chain 'A' and resid 899 through 900
    Processing sheet with id=AA7, first strand: chain 'A' and resid 921 through 924
    Processing sheet with id=AA8, first strand: chain 'A' and resid 949 through 956
      removed outlier: 3.587A  pdb=" N   GLY A1004 " --> pdb=" O   VAL A 939 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   ARG A 941 " --> pdb=" O   GLN A1002 " (cutoff:3.500A)
      removed outlier: 5.619A  pdb=" N   GLN A1002 " --> pdb=" O   ARG A 941 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1090 through 1093
      removed outlier: 6.390A  pdb=" N   ARG A1048 " --> pdb=" O   PHE A1043 " (cutoff:3.500A)
      removed outlier: 4.825A  pdb=" N   PHE A1043 " --> pdb=" O   ARG A1048 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   ASN A1050 " --> pdb=" O   THR A1041 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   GLU A1011 " --> pdb=" O   ILE A1106 " (cutoff:3.500A)

    434 hydrogen bonds defined for protein.
    1257 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      141 hydrogen bonds
      278 hydrogen bond angles
      0 basepair planarities
      55 basepair parallelities
      101 stacking parallelities
  Total time for adding SS restraints: 3.56

  Time building geometry restraints manager: 1.22 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2214
        1.33 -     1.45: 3804
        1.45 -     1.57: 6203
        1.57 -     1.69: 306
        1.69 -     1.81: 28
  Bond restraints: 12555
  Sorted by residual:
  bond pdb=" C3'   G B  97 "
       pdb=" O3'   G B  97 "
    ideal  model  delta    sigma   weight residual
    1.427  1.480 -0.053 1.50e-02 4.44e+03 1.25e+01
  bond pdb=" C3'  DA D  29 "
       pdb=" O3'  DA D  29 "
    ideal  model  delta    sigma   weight residual
    1.422  1.517 -0.095 3.00e-02 1.11e+03 1.01e+01
  bond pdb=" O3'   G B  97 "
       pdb=" P     A B  98 "
    ideal  model  delta    sigma   weight residual
    1.607  1.650 -0.043 1.50e-02 4.44e+03 8.35e+00
  bond pdb=" C3'  DA X   1 "
       pdb=" O3'  DA X   1 "
    ideal  model  delta    sigma   weight residual
    1.422  1.502 -0.080 3.00e-02 1.11e+03 7.18e+00
  bond pdb=" CB  TRP A1128 "
       pdb=" CG  TRP A1128 "
    ideal  model  delta    sigma   weight residual
    1.498  1.428  0.070 3.10e-02 1.04e+03 5.16e+00
  ... (remaining 12550 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.49: 17324
        2.49 -     4.99: 365
        4.99 -     7.48: 43
        7.48 -     9.97: 13
        9.97 -    12.47: 2
  Bond angle restraints: 17747
  Sorted by residual:
  angle pdb=" C3'   G B  97 "
        pdb=" O3'   G B  97 "
        pdb=" P     A B  98 "
      ideal   model   delta    sigma   weight residual
     120.20  132.67  -12.47 1.50e+00 4.44e-01 6.91e+01
  angle pdb=" C3'  DA D  29 "
        pdb=" O3'  DA D  29 "
        pdb=" P    DT D  30 "
      ideal   model   delta    sigma   weight residual
     120.20  127.99   -7.79 1.50e+00 4.44e-01 2.70e+01
  angle pdb=" N   GLU A 548 "
        pdb=" CA  GLU A 548 "
        pdb=" CB  GLU A 548 "
      ideal   model   delta    sigma   weight residual
     110.28  118.15   -7.87 1.55e+00 4.16e-01 2.58e+01
  angle pdb=" C3'   C B  96 "
        pdb=" O3'   C B  96 "
        pdb=" P     G B  97 "
      ideal   model   delta    sigma   weight residual
     120.20  127.44   -7.24 1.50e+00 4.44e-01 2.33e+01
  angle pdb=" O3'   G B  97 "
        pdb=" C3'   G B  97 "
        pdb=" C2'   G B  97 "
      ideal   model   delta    sigma   weight residual
     109.50  116.42   -6.92 1.50e+00 4.44e-01 2.13e+01
  ... (remaining 17742 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.86: 7052
       34.86 -    69.71: 493
       69.71 -   104.57: 46
      104.57 -   139.42: 2
      139.42 -   174.28: 2
  Dihedral angle restraints: 7595
    sinusoidal: 4399
      harmonic: 3196
  Sorted by residual:
  dihedral pdb=" O4'   A B  98 "
           pdb=" C2'   A B  98 "
           pdb=" C1'   A B  98 "
           pdb=" C3'   A B  98 "
      ideal   model   delta sinusoidal    sigma   weight residual
      25.00  -13.57   38.57     1      8.00e+00 1.56e-02 3.27e+01
  dihedral pdb=" C4'   A B  98 "
           pdb=" O4'   A B  98 "
           pdb=" C1'   A B  98 "
           pdb=" C2'   A B  98 "
      ideal   model   delta sinusoidal    sigma   weight residual
       3.00  -30.59   33.59     1      8.00e+00 1.56e-02 2.50e+01
  dihedral pdb=" C8  GTP B   1 "
           pdb=" C1' GTP B   1 "
           pdb=" N9  GTP B   1 "
           pdb=" O4' GTP B   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59   18.39   86.20     1      2.00e+01 2.50e-03 2.24e+01
  ... (remaining 7592 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.112: 1960
       0.112 -    0.225: 77
       0.225 -    0.337: 7
       0.337 -    0.449: 0
       0.449 -    0.562: 1
  Chirality restraints: 2045
  Sorted by residual:
  chirality pdb=" CG  LEU A1075 "
            pdb=" CB  LEU A1075 "
            pdb=" CD1 LEU A1075 "
            pdb=" CD2 LEU A1075 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.03   -0.56 2.00e-01 2.50e+01 7.88e+00
  chirality pdb=" CG  LEU A 399 "
            pdb=" CB  LEU A 399 "
            pdb=" CD1 LEU A 399 "
            pdb=" CD2 LEU A 399 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.27   -0.32 2.00e-01 2.50e+01 2.57e+00
  chirality pdb=" CB  ILE A 681 "
            pdb=" CA  ILE A 681 "
            pdb=" CG1 ILE A 681 "
            pdb=" CG2 ILE A 681 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.34    0.30 2.00e-01 2.50e+01 2.28e+00
  ... (remaining 2042 not shown)

  Planarity restraints: 1743
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A1128 "   -0.021 2.00e-02 2.50e+03   3.62e-02 3.27e+01
        pdb=" CG  TRP A1128 "    0.085 2.00e-02 2.50e+03
        pdb=" CD1 TRP A1128 "   -0.067 2.00e-02 2.50e+03
        pdb=" CD2 TRP A1128 "    0.009 2.00e-02 2.50e+03
        pdb=" NE1 TRP A1128 "    0.012 2.00e-02 2.50e+03
        pdb=" CE2 TRP A1128 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP A1128 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A1128 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A1128 "   -0.023 2.00e-02 2.50e+03
        pdb=" CH2 TRP A1128 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B  97 "   -0.020 2.00e-02 2.50e+03   3.05e-02 2.78e+01
        pdb=" N9    G B  97 "   -0.025 2.00e-02 2.50e+03
        pdb=" C8    G B  97 "    0.002 2.00e-02 2.50e+03
        pdb=" N7    G B  97 "    0.013 2.00e-02 2.50e+03
        pdb=" C5    G B  97 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    G B  97 "    0.056 2.00e-02 2.50e+03
        pdb=" O6    G B  97 "   -0.054 2.00e-02 2.50e+03
        pdb=" N1    G B  97 "   -0.013 2.00e-02 2.50e+03
        pdb=" C2    G B  97 "    0.041 2.00e-02 2.50e+03
        pdb=" N2    G B  97 "   -0.034 2.00e-02 2.50e+03
        pdb=" N3    G B  97 "    0.006 2.00e-02 2.50e+03
        pdb=" C4    G B  97 "    0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C B  88 "    0.044 2.00e-02 2.50e+03   3.33e-02 2.50e+01
        pdb=" N1    C B  88 "   -0.072 2.00e-02 2.50e+03
        pdb=" C2    C B  88 "    0.035 2.00e-02 2.50e+03
        pdb=" O2    C B  88 "   -0.011 2.00e-02 2.50e+03
        pdb=" N3    C B  88 "   -0.005 2.00e-02 2.50e+03
        pdb=" C4    C B  88 "   -0.028 2.00e-02 2.50e+03
        pdb=" N4    C B  88 "    0.025 2.00e-02 2.50e+03
        pdb=" C5    C B  88 "    0.012 2.00e-02 2.50e+03
        pdb=" C6    C B  88 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1740 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 244
        2.58 -     3.16: 9289
        3.16 -     3.74: 23681
        3.74 -     4.32: 32009
        4.32 -     4.90: 47097
  Nonbonded interactions: 112320
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A  18 "
            pdb="MG    MG A1203 "
     model   vdw
     2.000 2.170
  nonbonded pdb=" OP1   U B  78 "
            pdb="MG    MG B 204 "
     model   vdw
     2.002 2.170
  nonbonded pdb=" OP2  DC T  14 "
            pdb="MG    MG A1201 "
     model   vdw
     2.015 2.170
  nonbonded pdb=" OP3  DT D  28 "
            pdb="MG    MG A1203 "
     model   vdw
     2.025 2.170
  nonbonded pdb=" OP2  DT D  28 "
            pdb="MG    MG A1202 "
     model   vdw
     2.030 2.170
  ... (remaining 112315 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.780
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     13.560
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:9.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
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   0.095  12556  Z= 0.288
  Angle     :  0.908  12.468  17747  Z= 0.481
  Chirality :  0.054   0.562   2045
  Planarity :  0.008   0.081   1743
  Dihedral  : 20.179 174.276   5521
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.84 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.18 (0.23), residues: 1097
  helix:  0.16 (0.21), residues: 539
  sheet: -0.31 (0.56), residues: 82
  loop : -0.24 (0.26), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG A 801 
 TYR   0.019   0.003   TYR A 986 
 PHE   0.072   0.004   PHE A 363 
 TRP   0.085   0.003   TRP A1128 
 HIS   0.007   0.002   HIS A 946 

Details of bonding type rmsd
  covalent geometry    : bond        0.00625 (12555)
  covalent geometry    : angle       0.90822 (17747)
  hydrogen bonds       : bond        0.06600 (  575)
  hydrogen bonds       : angle       4.95389 ( 1535)
  Misc. bond           : bond        0.00085 (    1)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.381 
Fit side-chains
REVERT: A  311 ASN cc_start: 0.7667 (m-40) cc_final: 0.7338 (m-40)
REVERT: A  358 SER cc_start: 0.7626 (m) cc_final: 0.7420 (m)
REVERT: A  720 ARG cc_start: 0.6997 (ttp-170) cc_final: 0.6494 (ttp-170)
REVERT: A  723 ASP cc_start: 0.5636 (m-30) cc_final: 0.5329 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 116
  average time/residue: 0.9213
  time to fit residues: 112.8194
Evaluate side-chains
  90 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 108 optimal weight:    9.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    3.9990
   chunk 113 optimal weight:    8.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 123 optimal weight:    5.9990
   chunk 65 optimal weight:    0.0970
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   overall best weight:    2.4186

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

Flipped N/Q/H residues before XYZ refinement:
A 201 GLN
A 377 ASN
A1084 GLN
A1113 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.169859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.132692 restraints weight = 11249.175|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 1.17
r_work: 0.3214 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3099 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.0979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  12556  Z= 0.210
  Angle     :  0.636   8.845  17747  Z= 0.334
  Chirality :  0.041   0.282   2045
  Planarity :  0.006   0.077   1743
  Dihedral  : 21.539 179.942   3432
  Min Nonbonded Distance : 1.849

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  :  6.56 %
    Favored  : 92.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.84 %
    Cis-general     : 0.10 %
    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:  0.67 (0.24), residues: 1097
  helix:  1.00 (0.22), residues: 543
  sheet: -0.34 (0.55), residues: 87
  loop :  0.08 (0.27), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 775 
 TYR   0.020   0.002   TYR A 986 
 PHE   0.022   0.002   PHE A 282 
 TRP   0.017   0.002   TRP A1128 
 HIS   0.007   0.001   HIS A 603 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 (12555)
  covalent geometry    : angle       0.63596 (17747)
  hydrogen bonds       : bond        0.05313 (  575)
  hydrogen bonds       : angle       4.23001 ( 1535)
  Misc. bond           : bond        0.00058 (    1)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 0.356 
Fit side-chains
REVERT: A  311 ASN cc_start: 0.7708 (m-40) cc_final: 0.7104 (m-40)
REVERT: A  358 SER cc_start: 0.7693 (m) cc_final: 0.7447 (m)
REVERT: A  548 GLU cc_start: 0.6483 (OUTLIER) cc_final: 0.5471 (mp0)
REVERT: A  602 ARG cc_start: 0.7521 (mtp85) cc_final: 0.6991 (mtm-85)
REVERT: A  650 MET cc_start: 0.7790 (OUTLIER) cc_final: 0.7518 (ptm)
REVERT: A  720 ARG cc_start: 0.7154 (ttp-170) cc_final: 0.6414 (ttp-170)
REVERT: A  723 ASP cc_start: 0.5892 (m-30) cc_final: 0.5578 (m-30)
REVERT: A 1025 ASP cc_start: 0.6494 (t0) cc_final: 0.6280 (t70)
REVERT: A 1084 GLN cc_start: 0.6754 (pt0) cc_final: 0.6340 (mp10)
  outliers start: 12
  outliers final: 4
  residues processed: 99
  average time/residue: 0.8978
  time to fit residues: 94.0280
Evaluate side-chains
  94 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 88
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  548 GLU
Chi-restraints excluded: chain A residue  650 MET
Chi-restraints excluded: chain A residue  706 GLN
Chi-restraints excluded: chain A residue  731 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 122 optimal weight:    6.9990
   chunk 108 optimal weight:    3.9990
   chunk 112 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9980
   chunk 31 optimal weight:    9.9990
   chunk 34 optimal weight:    0.9990
   chunk 74 optimal weight:   10.0000
   chunk 52 optimal weight:    8.9990
   chunk 36 optimal weight:   10.0000
   chunk 82 optimal weight:    9.9990
   chunk 119 optimal weight:    9.9990
   overall best weight:    3.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 201 GLN
A 377 ASN
A1100 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.165264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.126496 restraints weight = 11124.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.3388 rms_B_bonded: 1.28
r_work: 0.3112 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2988 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.1211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050  12556  Z= 0.286
  Angle     :  0.694   9.260  17747  Z= 0.362
  Chirality :  0.045   0.250   2045
  Planarity :  0.006   0.053   1743
  Dihedral  : 21.577 176.471   3432
  Min Nonbonded Distance : 1.853

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  :  7.87 %
    Favored  : 90.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.84 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.71 (0.24), residues: 1097
  helix:  1.10 (0.22), residues: 543
  sheet: -0.61 (0.55), residues: 82
  loop :  0.08 (0.27), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 775 
 TYR   0.023   0.002   TYR A 986 
 PHE   0.023   0.002   PHE A 282 
 TRP   0.013   0.002   TRP A 161 
 HIS   0.007   0.001   HIS A 603 

Details of bonding type rmsd
  covalent geometry    : bond        0.00614 (12555)
  covalent geometry    : angle       0.69437 (17747)
  hydrogen bonds       : bond        0.05801 (  575)
  hydrogen bonds       : angle       4.29879 ( 1535)
  Misc. bond           : bond        0.00031 (    1)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.306 
Fit side-chains
REVERT: A  311 ASN cc_start: 0.7651 (m-40) cc_final: 0.7054 (m-40)
REVERT: A  358 SER cc_start: 0.7861 (m) cc_final: 0.7633 (m)
REVERT: A  548 GLU cc_start: 0.6324 (OUTLIER) cc_final: 0.4921 (mp0)
REVERT: A  602 ARG cc_start: 0.7694 (mtp85) cc_final: 0.7086 (mtm-85)
REVERT: A  662 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.7230 (mtpt)
REVERT: A  720 ARG cc_start: 0.7154 (ttp-170) cc_final: 0.6427 (ttp-170)
REVERT: A  747 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.7377 (mtp85)
  outliers start: 17
  outliers final: 4
  residues processed: 99
  average time/residue: 0.8976
  time to fit residues: 93.9768
Evaluate side-chains
  93 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 86
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  548 GLU
Chi-restraints excluded: chain A residue  655 ASP
Chi-restraints excluded: chain A residue  662 LYS
Chi-restraints excluded: chain A residue  731 SER
Chi-restraints excluded: chain A residue  747 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 114 optimal weight:    7.9990
   chunk 88 optimal weight:    1.9990
   chunk 4 optimal weight:    5.9990
   chunk 3 optimal weight:    5.9990
   chunk 12 optimal weight:    0.8980
   chunk 94 optimal weight:    0.1980
   chunk 109 optimal weight:    6.9990
   chunk 101 optimal weight:    7.9990
   chunk 122 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9990
   chunk 18 optimal weight:    4.9990
   overall best weight:    1.8186

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

Flipped N/Q/H residues before XYZ refinement:
A 201 GLN
A 377 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.167780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.129357 restraints weight = 11086.415|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 1.25
r_work: 0.3154 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3030 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8368
moved from start:          0.1215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12556  Z= 0.175
  Angle     :  0.590   9.200  17747  Z= 0.309
  Chirality :  0.039   0.231   2045
  Planarity :  0.005   0.050   1743
  Dihedral  : 21.431 171.154   3432
  Min Nonbonded Distance : 1.891

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  :  8.85 %
    Favored  : 89.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.84 %
    Cis-general     : 0.10 %
    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:  1.03 (0.25), residues: 1097
  helix:  1.40 (0.22), residues: 546
  sheet: -0.47 (0.58), residues: 76
  loop :  0.18 (0.28), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 659 
 TYR   0.017   0.002   TYR A 986 
 PHE   0.019   0.002   PHE A 282 
 TRP   0.012   0.002   TRP A 161 
 HIS   0.004   0.001   HIS A 749 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 (12555)
  covalent geometry    : angle       0.59034 (17747)
  hydrogen bonds       : bond        0.04856 (  575)
  hydrogen bonds       : angle       4.06355 ( 1535)
  Misc. bond           : bond        0.00046 (    1)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 86
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
REVERT: A  217 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7704 (mp0)
REVERT: A  311 ASN cc_start: 0.7598 (m-40) cc_final: 0.6921 (m-40)
REVERT: A  358 SER cc_start: 0.7771 (m) cc_final: 0.7532 (m)
REVERT: A  602 ARG cc_start: 0.7616 (mtp85) cc_final: 0.7310 (mtt-85)
REVERT: A  662 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.7208 (mtpt)
REVERT: A  701 LYS cc_start: 0.7303 (OUTLIER) cc_final: 0.7076 (mttt)
REVERT: A  720 ARG cc_start: 0.7227 (ttp-170) cc_final: 0.6477 (ttp-170)
REVERT: A  747 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7296 (mtp85)
REVERT: A 1025 ASP cc_start: 0.6554 (t0) cc_final: 0.6270 (t70)
  outliers start: 14
  outliers final: 4
  residues processed: 95
  average time/residue: 0.9374
  time to fit residues: 93.9024
Evaluate side-chains
  93 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 86
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  548 GLU
Chi-restraints excluded: chain A residue  655 ASP
Chi-restraints excluded: chain A residue  662 LYS
Chi-restraints excluded: chain A residue  701 LYS
Chi-restraints excluded: chain A residue  731 SER
Chi-restraints excluded: chain A residue  747 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 44 optimal weight:    7.9990
   chunk 116 optimal weight:   20.0000
   chunk 57 optimal weight:    9.9990
   chunk 40 optimal weight:    9.9990
   chunk 86 optimal weight:    5.9990
   chunk 45 optimal weight:    0.7980
   chunk 76 optimal weight:    5.9990
   chunk 122 optimal weight:    6.9990
   chunk 64 optimal weight:    8.9990
   chunk 78 optimal weight:    3.9990
   chunk 24 optimal weight:    5.9990
   overall best weight:    4.5588

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

Flipped N/Q/H residues before XYZ refinement:
A 201 GLN
A 377 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.164371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.125624 restraints weight = 11162.569|
|-----------------------------------------------------------------------------|
r_work (start): 0.3377 rms_B_bonded: 1.30
r_work: 0.3102 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2979 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8422
moved from start:          0.1375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.054  12556  Z= 0.325
  Angle     :  0.726   9.288  17747  Z= 0.377
  Chirality :  0.047   0.240   2045
  Planarity :  0.006   0.063   1743
  Dihedral  : 21.559 173.004   3432
  Min Nonbonded Distance : 1.845

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  :  8.31 %
    Favored  : 89.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.84 %
    Cis-general     : 0.10 %
    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:  0.76 (0.24), residues: 1097
  helix:  1.14 (0.22), residues: 546
  sheet: -0.73 (0.54), residues: 82
  loop :  0.12 (0.28), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 165 
 TYR   0.025   0.003   TYR A 986 
 PHE   0.023   0.003   PHE A 282 
 TRP   0.015   0.002   TRP A  13 
 HIS   0.007   0.002   HIS A1100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00699 (12555)
  covalent geometry    : angle       0.72621 (17747)
  hydrogen bonds       : bond        0.05981 (  575)
  hydrogen bonds       : angle       4.31920 ( 1535)
  Misc. bond           : bond        0.00026 (    1)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 84
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
REVERT: A  137 ARG cc_start: 0.9198 (OUTLIER) cc_final: 0.6497 (mtt180)
REVERT: A  191 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7913 (ttt-90)
REVERT: A  311 ASN cc_start: 0.7687 (m-40) cc_final: 0.6979 (m-40)
REVERT: A  358 SER cc_start: 0.7876 (m) cc_final: 0.7666 (m)
REVERT: A  602 ARG cc_start: 0.7740 (mtp85) cc_final: 0.7366 (mtt-85)
REVERT: A  662 LYS cc_start: 0.7558 (OUTLIER) cc_final: 0.7254 (mtpt)
REVERT: A  701 LYS cc_start: 0.7391 (OUTLIER) cc_final: 0.7137 (mttt)
REVERT: A  720 ARG cc_start: 0.7167 (ttp-170) cc_final: 0.6465 (ttp-170)
REVERT: A  747 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.7336 (mtp85)
REVERT: A  847 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7808 (mm-30)
REVERT: A 1025 ASP cc_start: 0.6470 (t0) cc_final: 0.6174 (t70)
REVERT: A 1084 GLN cc_start: 0.6962 (pt0) cc_final: 0.6455 (mp10)
  outliers start: 23
  outliers final: 8
  residues processed: 101
  average time/residue: 0.8782
  time to fit residues: 93.8785
Evaluate side-chains
  96 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 GLU
Chi-restraints excluded: chain A residue  137 ARG
Chi-restraints excluded: chain A residue  191 ARG
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  482 GLU
Chi-restraints excluded: chain A residue  548 GLU
Chi-restraints excluded: chain A residue  655 ASP
Chi-restraints excluded: chain A residue  662 LYS
Chi-restraints excluded: chain A residue  672 THR
Chi-restraints excluded: chain A residue  701 LYS
Chi-restraints excluded: chain A residue  731 SER
Chi-restraints excluded: chain A residue  747 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 100 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 109 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   chunk 52 optimal weight:    6.9990
   chunk 60 optimal weight:    6.9990
   chunk 77 optimal weight:    3.9990
   chunk 84 optimal weight:    4.9990
   chunk 97 optimal weight:    0.9990
   chunk 111 optimal weight:    4.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 377 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.167384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.128371 restraints weight = 11038.192|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 1.23
r_work: 0.3152 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3031 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.1327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12556  Z= 0.183
  Angle     :  0.601   9.304  17747  Z= 0.313
  Chirality :  0.040   0.232   2045
  Planarity :  0.005   0.061   1743
  Dihedral  : 21.459 168.002   3432
  Min Nonbonded Distance : 1.888

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 10.27 %
    Favored  : 88.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.84 %
    Cis-general     : 0.10 %
    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:  1.07 (0.25), residues: 1097
  helix:  1.42 (0.22), residues: 547
  sheet: -0.58 (0.57), residues: 76
  loop :  0.22 (0.28), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1048 
 TYR   0.017   0.002   TYR A 986 
 PHE   0.019   0.002   PHE A 282 
 TRP   0.012   0.002   TRP A 161 
 HIS   0.005   0.001   HIS A 749 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 (12555)
  covalent geometry    : angle       0.60064 (17747)
  hydrogen bonds       : bond        0.04849 (  575)
  hydrogen bonds       : angle       4.07829 ( 1535)
  Misc. bond           : bond        0.00047 (    1)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
REVERT: A  191 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.8003 (ttt-90)
REVERT: A  217 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7709 (mp0)
REVERT: A  311 ASN cc_start: 0.7626 (m-40) cc_final: 0.6955 (m-40)
REVERT: A  358 SER cc_start: 0.7762 (m) cc_final: 0.7535 (m)
REVERT: A  602 ARG cc_start: 0.7639 (mtp85) cc_final: 0.7207 (mtt-85)
REVERT: A  701 LYS cc_start: 0.7318 (OUTLIER) cc_final: 0.7088 (mttt)
REVERT: A  747 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.7278 (mtp85)
REVERT: A  847 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7649 (mm-30)
REVERT: A 1025 ASP cc_start: 0.6433 (t0) cc_final: 0.6223 (t70)
  outliers start: 13
  outliers final: 6
  residues processed: 96
  average time/residue: 0.8858
  time to fit residues: 89.8825
Evaluate side-chains
  95 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 ARG
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  548 GLU
Chi-restraints excluded: chain A residue  655 ASP
Chi-restraints excluded: chain A residue  672 THR
Chi-restraints excluded: chain A residue  701 LYS
Chi-restraints excluded: chain A residue  731 SER
Chi-restraints excluded: chain A residue  747 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 77 optimal weight:    9.9990
   chunk 74 optimal weight:    4.9990
   chunk 59 optimal weight:    5.9990
   chunk 53 optimal weight:    8.9990
   chunk 88 optimal weight:    6.9990
   chunk 79 optimal weight:    3.9990
   chunk 25 optimal weight:    9.9990
   chunk 101 optimal weight:    9.9990
   chunk 73 optimal weight:    2.9990
   chunk 41 optimal weight:    5.9990
   chunk 69 optimal weight:    3.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 377 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.164674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.125857 restraints weight = 11009.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.3378 rms_B_bonded: 1.27
r_work: 0.3106 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2983 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8418
moved from start:          0.1439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.050  12556  Z= 0.314
  Angle     :  0.714   9.362  17747  Z= 0.371
  Chirality :  0.046   0.235   2045
  Planarity :  0.006   0.059   1743
  Dihedral  : 21.557 170.592   3432
  Min Nonbonded Distance : 1.845

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 10.82 %
    Favored  : 87.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.84 %
    Cis-general     : 0.10 %
    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:  0.81 (0.25), residues: 1097
  helix:  1.19 (0.22), residues: 546
  sheet: -0.75 (0.53), residues: 82
  loop :  0.15 (0.28), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 165 
 TYR   0.024   0.003   TYR A 986 
 PHE   0.022   0.003   PHE A 282 
 TRP   0.014   0.002   TRP A  13 
 HIS   0.006   0.001   HIS A1100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00675 (12555)
  covalent geometry    : angle       0.71431 (17747)
  hydrogen bonds       : bond        0.05793 (  575)
  hydrogen bonds       : angle       4.28987 ( 1535)
  Misc. bond           : bond        0.00032 (    1)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 81
  time to evaluate  : 0.348 
Fit side-chains
REVERT: A  137 ARG cc_start: 0.9191 (OUTLIER) cc_final: 0.6453 (mtt180)
REVERT: A  191 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.8010 (ttt-90)
REVERT: A  311 ASN cc_start: 0.7664 (m-40) cc_final: 0.6980 (m-40)
REVERT: A  358 SER cc_start: 0.7822 (m) cc_final: 0.7608 (m)
REVERT: A  548 GLU cc_start: 0.6415 (OUTLIER) cc_final: 0.5136 (mp0)
REVERT: A  602 ARG cc_start: 0.7697 (mtp85) cc_final: 0.7339 (mtt-85)
REVERT: A  662 LYS cc_start: 0.7516 (OUTLIER) cc_final: 0.7225 (mtpt)
REVERT: A  701 LYS cc_start: 0.7370 (OUTLIER) cc_final: 0.7145 (mttt)
REVERT: A  747 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.7320 (mtp85)
REVERT: A  847 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7792 (mm-30)
REVERT: A 1025 ASP cc_start: 0.6469 (t0) cc_final: 0.6222 (t70)
  outliers start: 17
  outliers final: 6
  residues processed: 95
  average time/residue: 0.8533
  time to fit residues: 85.7223
Evaluate side-chains
  93 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 ARG
Chi-restraints excluded: chain A residue  191 ARG
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  482 GLU
Chi-restraints excluded: chain A residue  548 GLU
Chi-restraints excluded: chain A residue  655 ASP
Chi-restraints excluded: chain A residue  662 LYS
Chi-restraints excluded: chain A residue  672 THR
Chi-restraints excluded: chain A residue  701 LYS
Chi-restraints excluded: chain A residue  731 SER
Chi-restraints excluded: chain A residue  747 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 36 optimal weight:    5.9990
   chunk 70 optimal weight:    5.9990
   chunk 50 optimal weight:    8.9990
   chunk 117 optimal weight:    4.9990
   chunk 69 optimal weight:    6.9990
   chunk 118 optimal weight:   10.0000
   chunk 110 optimal weight:    6.9990
   chunk 6 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   chunk 86 optimal weight:    7.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    3.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 377 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.165306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.125864 restraints weight = 10997.021|
|-----------------------------------------------------------------------------|
r_work (start): 0.3374 rms_B_bonded: 1.33
r_work: 0.3125 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3004 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8381
moved from start:          0.1433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045  12556  Z= 0.268
  Angle     :  0.675   9.456  17747  Z= 0.351
  Chirality :  0.044   0.234   2045
  Planarity :  0.006   0.060   1743
  Dihedral  : 21.550 169.186   3432
  Min Nonbonded Distance : 1.850

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 11.15 %
    Favored  : 87.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.84 %
    Cis-general     : 0.10 %
    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:  0.82 (0.25), residues: 1097
  helix:  1.18 (0.22), residues: 547
  sheet: -0.61 (0.56), residues: 76
  loop :  0.14 (0.28), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 659 
 TYR   0.022   0.002   TYR A 986 
 PHE   0.022   0.002   PHE A 282 
 TRP   0.013   0.002   TRP A 161 
 HIS   0.005   0.001   HIS A 749 

Details of bonding type rmsd
  covalent geometry    : bond        0.00576 (12555)
  covalent geometry    : angle       0.67525 (17747)
  hydrogen bonds       : bond        0.05462 (  575)
  hydrogen bonds       : angle       4.23674 ( 1535)
  Misc. bond           : bond        0.00037 (    1)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 83
  time to evaluate  : 0.378 
Fit side-chains
REVERT: A  137 ARG cc_start: 0.9184 (OUTLIER) cc_final: 0.6392 (mtt180)
REVERT: A  191 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.8000 (ttt-90)
REVERT: A  311 ASN cc_start: 0.7634 (m-40) cc_final: 0.6901 (m-40)
REVERT: A  358 SER cc_start: 0.7811 (m) cc_final: 0.7595 (m)
REVERT: A  548 GLU cc_start: 0.6297 (OUTLIER) cc_final: 0.4841 (mp0)
REVERT: A  602 ARG cc_start: 0.7641 (mtp85) cc_final: 0.7263 (mtt-85)
REVERT: A  662 LYS cc_start: 0.7500 (OUTLIER) cc_final: 0.7203 (mtpt)
REVERT: A  701 LYS cc_start: 0.7313 (OUTLIER) cc_final: 0.7099 (mttt)
REVERT: A  720 ARG cc_start: 0.7166 (ttp-170) cc_final: 0.6491 (ttp-170)
REVERT: A  747 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.7301 (mtp85)
REVERT: A  847 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7765 (mm-30)
REVERT: A 1025 ASP cc_start: 0.6455 (t0) cc_final: 0.6239 (t70)
REVERT: A 1084 GLN cc_start: 0.6951 (pt0) cc_final: 0.6479 (mp-120)
  outliers start: 16
  outliers final: 7
  residues processed: 97
  average time/residue: 0.8861
  time to fit residues: 90.9558
Evaluate side-chains
  95 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 82
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 ARG
Chi-restraints excluded: chain A residue  191 ARG
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  482 GLU
Chi-restraints excluded: chain A residue  548 GLU
Chi-restraints excluded: chain A residue  650 MET
Chi-restraints excluded: chain A residue  655 ASP
Chi-restraints excluded: chain A residue  662 LYS
Chi-restraints excluded: chain A residue  672 THR
Chi-restraints excluded: chain A residue  701 LYS
Chi-restraints excluded: chain A residue  731 SER
Chi-restraints excluded: chain A residue  747 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 32 optimal weight:   10.0000
   chunk 98 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   chunk 78 optimal weight:    9.9990
   chunk 74 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 95 optimal weight:    1.9990
   chunk 50 optimal weight:    6.9990
   chunk 115 optimal weight:    6.9990
   chunk 111 optimal weight:    5.9990
   chunk 52 optimal weight:    7.9990
   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 377 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.166261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.127235 restraints weight = 11003.110|
|-----------------------------------------------------------------------------|
r_work (start): 0.3393 rms_B_bonded: 1.33
r_work: 0.3143 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3021 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.1416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  12556  Z= 0.214
  Angle     :  0.634   9.466  17747  Z= 0.331
  Chirality :  0.041   0.233   2045
  Planarity :  0.005   0.061   1743
  Dihedral  : 21.537 168.011   3432
  Min Nonbonded Distance : 1.875

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 11.37 %
    Favored  : 87.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.84 %
    Cis-general     : 0.10 %
    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:  0.96 (0.25), residues: 1097
  helix:  1.31 (0.22), residues: 547
  sheet: -0.63 (0.56), residues: 76
  loop :  0.20 (0.28), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 659 
 TYR   0.020   0.002   TYR A 986 
 PHE   0.020   0.002   PHE A 282 
 TRP   0.013   0.002   TRP A 161 
 HIS   0.005   0.001   HIS A 749 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 (12555)
  covalent geometry    : angle       0.63425 (17747)
  hydrogen bonds       : bond        0.05156 (  575)
  hydrogen bonds       : angle       4.17537 ( 1535)
  Misc. bond           : bond        0.00054 (    1)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 82
  time to evaluate  : 0.387 
Fit side-chains
REVERT: A  137 ARG cc_start: 0.9161 (OUTLIER) cc_final: 0.6366 (mtt180)
REVERT: A  191 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.8035 (ttt-90)
REVERT: A  217 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7622 (mp0)
REVERT: A  311 ASN cc_start: 0.7620 (m-40) cc_final: 0.6912 (m-40)
REVERT: A  358 SER cc_start: 0.7788 (m) cc_final: 0.7567 (m)
REVERT: A  377 ASN cc_start: 0.6078 (m-40) cc_final: 0.5827 (m110)
REVERT: A  548 GLU cc_start: 0.6321 (OUTLIER) cc_final: 0.4882 (mp0)
REVERT: A  602 ARG cc_start: 0.7630 (mtp85) cc_final: 0.7205 (mtt-85)
REVERT: A  662 LYS cc_start: 0.7475 (OUTLIER) cc_final: 0.7175 (mtpt)
REVERT: A  701 LYS cc_start: 0.7310 (OUTLIER) cc_final: 0.7084 (mttt)
REVERT: A  720 ARG cc_start: 0.7161 (ttp-170) cc_final: 0.6476 (ttp-170)
REVERT: A  747 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.7268 (mtp85)
REVERT: A  847 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7752 (mm-30)
REVERT: A 1025 ASP cc_start: 0.6381 (t0) cc_final: 0.6170 (t70)
REVERT: A 1084 GLN cc_start: 0.6932 (pt0) cc_final: 0.6436 (mp10)
  outliers start: 13
  outliers final: 6
  residues processed: 95
  average time/residue: 0.8935
  time to fit residues: 89.7062
Evaluate side-chains
  94 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 82
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 ARG
Chi-restraints excluded: chain A residue  191 ARG
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  482 GLU
Chi-restraints excluded: chain A residue  548 GLU
Chi-restraints excluded: chain A residue  655 ASP
Chi-restraints excluded: chain A residue  662 LYS
Chi-restraints excluded: chain A residue  672 THR
Chi-restraints excluded: chain A residue  701 LYS
Chi-restraints excluded: chain A residue  731 SER
Chi-restraints excluded: chain A residue  747 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 106 optimal weight:    0.8980
   chunk 32 optimal weight:    7.9990
   chunk 45 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 80 optimal weight:    0.7980
   chunk 5 optimal weight:    3.9990
   chunk 26 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9990
   chunk 94 optimal weight:    4.9990
   chunk 92 optimal weight:    1.9990
   chunk 28 optimal weight:    5.9990
   overall best weight:    1.5386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.168495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.129519 restraints weight = 11121.770|
|-----------------------------------------------------------------------------|
r_work (start): 0.3424 rms_B_bonded: 1.24
r_work: 0.3173 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3049 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.1411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12556  Z= 0.163
  Angle     :  0.580   9.133  17747  Z= 0.302
  Chirality :  0.039   0.236   2045
  Planarity :  0.005   0.052   1743
  Dihedral  : 21.395 164.271   3432
  Min Nonbonded Distance : 1.905

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 11.48 %
    Favored  : 86.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.84 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.20 (0.25), residues: 1097
  helix:  1.54 (0.22), residues: 547
  sheet: -0.49 (0.56), residues: 76
  loop :  0.28 (0.28), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 659 
 TYR   0.016   0.002   TYR A 986 
 PHE   0.018   0.002   PHE A 282 
 TRP   0.012   0.001   TRP A 161 
 HIS   0.005   0.001   HIS A 749 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 (12555)
  covalent geometry    : angle       0.58032 (17747)
  hydrogen bonds       : bond        0.04491 (  575)
  hydrogen bonds       : angle       3.98641 ( 1535)
  Misc. bond           : bond        0.00050 (    1)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 86
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
REVERT: A  137 ARG cc_start: 0.9111 (OUTLIER) cc_final: 0.6369 (mtt180)
REVERT: A  191 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7996 (ttt-90)
REVERT: A  217 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7640 (mp0)
REVERT: A  311 ASN cc_start: 0.7645 (m-40) cc_final: 0.6991 (m-40)
REVERT: A  358 SER cc_start: 0.7817 (m) cc_final: 0.7608 (m)
REVERT: A  602 ARG cc_start: 0.7631 (mtp85) cc_final: 0.7257 (mtt-85)
REVERT: A  662 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.7175 (mtpt)
REVERT: A  720 ARG cc_start: 0.7266 (ttp-170) cc_final: 0.6552 (ttp-170)
REVERT: A  747 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.7276 (mtp85)
REVERT: A  847 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7689 (mm-30)
REVERT: A  880 ARG cc_start: 0.6728 (ptt90) cc_final: 0.6504 (ptt90)
  outliers start: 14
  outliers final: 6
  residues processed: 97
  average time/residue: 0.8720
  time to fit residues: 89.6979
Evaluate side-chains
  92 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 ARG
Chi-restraints excluded: chain A residue  191 ARG
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  548 GLU
Chi-restraints excluded: chain A residue  655 ASP
Chi-restraints excluded: chain A residue  662 LYS
Chi-restraints excluded: chain A residue  672 THR
Chi-restraints excluded: chain A residue  731 SER
Chi-restraints excluded: chain A residue  747 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 15 optimal weight:    6.9990
   chunk 48 optimal weight:    6.9990
   chunk 84 optimal weight:    6.9990
   chunk 66 optimal weight:    6.9990
   chunk 91 optimal weight:   10.0000
   chunk 101 optimal weight:    5.9990
   chunk 63 optimal weight:    0.1980
   chunk 3 optimal weight:    9.9990
   chunk 82 optimal weight:    9.9990
   chunk 27 optimal weight:    7.9990
   overall best weight:    4.6388

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

Flipped N/Q/H residues before XYZ refinement:
A 201 GLN
A 377 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.164672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.125287 restraints weight = 10952.120|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 1.34
r_work: 0.3115 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2998 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8390
moved from start:          0.1493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.051  12556  Z= 0.326
  Angle     :  0.722   9.350  17747  Z= 0.374
  Chirality :  0.046   0.234   2045
  Planarity :  0.006   0.058   1743
  Dihedral  : 21.550 169.013   3432
  Min Nonbonded Distance : 1.845

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 12.57 %
    Favored  : 86.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.84 %
    Cis-general     : 0.10 %
    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:  0.84 (0.25), residues: 1097
  helix:  1.20 (0.22), residues: 546
  sheet: -0.68 (0.53), residues: 82
  loop :  0.18 (0.28), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 165 
 TYR   0.024   0.003   TYR A 986 
 PHE   0.022   0.003   PHE A 282 
 TRP   0.016   0.003   TRP A1128 
 HIS   0.006   0.002   HIS A1100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00701 (12555)
  covalent geometry    : angle       0.72151 (17747)
  hydrogen bonds       : bond        0.05756 (  575)
  hydrogen bonds       : angle       4.28142 ( 1535)
  Misc. bond           : bond        0.00021 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4731.03 seconds
wall clock time: 81 minutes 9.65 seconds (4869.65 seconds total)