Starting phenix.real_space_refine
on Tue Mar  3 20:52:44 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d2o_27144/03_2026/8d2o_27144.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d2o_27144/03_2026/8d2o_27144.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.66
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d2o_27144/03_2026/8d2o_27144.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d2o_27144/03_2026/8d2o_27144.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8d2o_27144/03_2026/8d2o_27144.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d2o_27144/03_2026/8d2o_27144.map"
  }
  resolution = 2.66
  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=   0.005
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     122      5.49       5
     Mg      5      5.21       5
     S      10      5.16       5
     C    4878      2.51       5
     N    1567      2.21       5
     O    1889      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8471
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 5872
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 749, 5872
          Classifications: {'peptide': 749}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'CIS': 2, 'PCIS': 3, 'PTRANS': 44, 'TRANS': 699}
          Chain breaks: 4
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 59
          Unresolved non-hydrogen dihedrals: 43
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1, 'PHE:plan': 1, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 34
    Chain: "B"
      Number of atoms: 1855
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 87, 1855
          Classifications: {'RNA': 87}
          Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 5, 'rna3p_pur': 39, 'rna3p_pyr': 38}
          Link IDs: {'rna2p': 10, 'rna3p': 76}
          Chain breaks: 2
    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: 226
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 226
          Classifications: {'DNA': 11}
          Modifications used: {'p5*END': 1}
          Link IDs: {'rna3p': 10}
    Chain: "D"
      Number of atoms: 243
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 243
          Classifications: {'DNA': 12}
          Link IDs: {'rna3p': 11}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {' MG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "A"
      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: 2.28, per 1000 atoms: 0.27
  Number of scatterers: 8471
  At special positions: 0
  Unit cell: (91.575, 94.875, 119.625, 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      10     16.00
     P     122     15.00
     Mg      5     11.99
     O    1889      8.00
     N    1567      7.00
     C    4878      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.79
  Conformation dependent library (CDL) restraints added in 224.3 milliseconds
  

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1396

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 7 sheets defined
      44.7% alpha, 12.8% beta
      43 base pairs and 81 stacking pairs defined.
    Time for finding SS restraints: 1.21
  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
      removed outlier: 3.544A  pdb=" N   VAL A 225 " --> pdb=" O   ARG A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 239 through 251
    Processing helix  chain 'A' and resid 486 through 508
    Processing helix  chain 'A' and resid 685 through 703
    Processing helix  chain 'A' and resid 713 through 722
      removed outlier: 3.833A  pdb=" N   GLU A 717 " --> pdb=" O   GLY A 713 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   LEU A 722 " --> pdb=" O   ALA A 718 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 725 through 730
    Processing helix  chain 'A' and resid 742 through 747
      removed outlier: 3.708A  pdb=" N   LEU A 745 " --> pdb=" O   THR A 742 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   ASP A 746 " --> pdb=" O   LYS A 743 " (cutoff:3.500A)
      removed outlier: 5.012A  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 759
      removed outlier: 3.796A  pdb=" N   THR A 759 " --> pdb=" O   VAL A 755 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 761 through 782
      removed outlier: 4.112A  pdb=" N   SER A 777 " --> pdb=" O   SER A 773 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ALA A 778 " --> pdb=" O   ARG A 774 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 797 through 807
    Processing helix  chain 'A' and resid 809 through 820
      removed outlier: 3.688A  pdb=" N   ARG A 820 " --> pdb=" O   SER A 816 " (cutoff:3.500A)
    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 1024 through 1033
      removed outlier: 3.793A  pdb=" N   MET A1028 " --> pdb=" O   GLY A1024 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   TYR A1032 " --> pdb=" O   MET A1028 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1058 through 1071
    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: 6.172A  pdb=" N   ILE A 513 " --> pdb=" O   ALA A 708 " (cutoff:3.500A)
      removed outlier: 7.605A  pdb=" N   PHE A 710 " --> pdb=" O   ILE A 513 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   VAL A 515 " --> pdb=" O   PHE A 710 " (cutoff:3.500A)
      removed outlier: 7.544A  pdb=" N   TRP A  13 " --> pdb=" O   SER A 512 " (cutoff:3.500A)
      removed outlier: 8.934A  pdb=" N   VAL A 514 " --> pdb=" O   TRP A  13 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   LEU A  15 " --> pdb=" O   VAL A 514 " (cutoff:3.500A)
      removed outlier: 7.923A  pdb=" N   GLU A 516 " --> pdb=" O   LEU A  15 " (cutoff:3.500A)
      removed outlier: 6.840A  pdb=" N   VAL A  17 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   SER A  30 " --> pdb=" O   ILE A  39 " (cutoff:3.500A)
      removed outlier: 5.367A  pdb=" N   ILE A  39 " --> pdb=" O   SER A  30 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 846 through 849
    Processing sheet with id=AA3, first strand: chain 'A' and resid 854 through 855
    Processing sheet with id=AA4, first strand: chain 'A' and resid 899 through 900
    Processing sheet with id=AA5, first strand: chain 'A' and resid 921 through 924
    Processing sheet with id=AA6, first strand: chain 'A' and resid 948 through 956
      removed outlier: 3.726A  pdb=" N   GLY A1004 " --> pdb=" O   VAL A 939 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   ARG A 941 " --> pdb=" O   GLN A1002 " (cutoff:3.500A)
      removed outlier: 5.858A  pdb=" N   GLN A1002 " --> pdb=" O   ARG A 941 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1090 through 1093
      removed outlier: 6.798A  pdb=" N   ARG A1048 " --> pdb=" O   PHE A1043 " (cutoff:3.500A)
      removed outlier: 4.972A  pdb=" N   PHE A1043 " --> pdb=" O   ARG A1048 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   ASN A1050 " --> pdb=" O   THR A1041 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   GLU A1011 " --> pdb=" O   ILE A1106 " (cutoff:3.500A)

    271 hydrogen bonds defined for protein.
    795 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      109 hydrogen bonds
      210 hydrogen bond angles
      0 basepair planarities
      43 basepair parallelities
      81 stacking parallelities
  Total time for adding SS restraints: 1.89

  Time building geometry restraints manager: 0.98 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: 2029
        1.33 -     1.46: 2676
        1.46 -     1.58: 3942
        1.58 -     1.70: 241
        1.70 -     1.82: 15
  Bond restraints: 8903
  Sorted by residual:
  bond pdb=" C3'   G B  95 "
       pdb=" O3'   G B  95 "
    ideal  model  delta    sigma   weight residual
    1.427  1.464 -0.037 1.50e-02 4.44e+03 6.24e+00
  bond pdb=" C3'  DC D  35 "
       pdb=" O3'  DC D  35 "
    ideal  model  delta    sigma   weight residual
    1.422  1.486 -0.064 3.00e-02 1.11e+03 4.58e+00
  bond pdb=" C3'  DA D  36 "
       pdb=" O3'  DA D  36 "
    ideal  model  delta    sigma   weight residual
    1.422  1.484 -0.062 3.00e-02 1.11e+03 4.34e+00
  bond pdb=" CB  PRO A1087 "
       pdb=" CG  PRO A1087 "
    ideal  model  delta    sigma   weight residual
    1.506  1.584 -0.078 3.90e-02 6.57e+02 3.99e+00
  bond pdb=" CG  PRO A1087 "
       pdb=" CD  PRO A1087 "
    ideal  model  delta    sigma   weight residual
    1.512  1.459  0.053 2.70e-02 1.37e+03 3.91e+00
  ... (remaining 8898 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.16: 12264
        2.16 -     4.32: 324
        4.32 -     6.48: 50
        6.48 -     8.64: 15
        8.64 -    10.80: 2
  Bond angle restraints: 12655
  Sorted by residual:
  angle pdb=" CA  PRO A1087 "
        pdb=" N   PRO A1087 "
        pdb=" CD  PRO A1087 "
      ideal   model   delta    sigma   weight residual
     111.50  104.00    7.50 1.40e+00 5.10e-01 2.87e+01
  angle pdb=" C3'   G B  95 "
        pdb=" O3'   G B  95 "
        pdb=" P     C B  96 "
      ideal   model   delta    sigma   weight residual
     120.20  127.33   -7.13 1.50e+00 4.44e-01 2.26e+01
  angle pdb=" CG  ARG A  14 "
        pdb=" CD  ARG A  14 "
        pdb=" NE  ARG A  14 "
      ideal   model   delta    sigma   weight residual
     112.00  122.09  -10.09 2.20e+00 2.07e-01 2.10e+01
  angle pdb=" O3'   G B  14 "
        pdb=" C3'   G B  14 "
        pdb=" C2'   G B  14 "
      ideal   model   delta    sigma   weight residual
     113.70  120.39   -6.69 1.50e+00 4.44e-01 1.99e+01
  angle pdb=" O3'   G B  95 "
        pdb=" C3'   G B  95 "
        pdb=" C2'   G B  95 "
      ideal   model   delta    sigma   weight residual
     109.50  115.97   -6.47 1.50e+00 4.44e-01 1.86e+01
  ... (remaining 12650 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.19: 4935
       34.19 -    68.39: 391
       68.39 -   102.58: 39
      102.58 -   136.77: 2
      136.77 -   170.96: 4
  Dihedral angle restraints: 5371
    sinusoidal: 3218
      harmonic: 2153
  Sorted by residual:
  dihedral pdb=" O4'   C B  96 "
           pdb=" C1'   C B  96 "
           pdb=" N1    C B  96 "
           pdb=" C2    C B  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00  -55.68  -72.32     1      1.70e+01 3.46e-03 2.31e+01
  dihedral pdb=" CA  ARG A1091 "
           pdb=" C   ARG A1091 "
           pdb=" N   ALA A1092 "
           pdb=" CA  ALA A1092 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.62  -23.38     0      5.00e+00 4.00e-02 2.19e+01
  dihedral pdb=" CA  GLN A 511 "
           pdb=" C   GLN A 511 "
           pdb=" N   SER A 512 "
           pdb=" CA  SER A 512 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.04   20.96     0      5.00e+00 4.00e-02 1.76e+01
  ... (remaining 5368 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 1306
       0.070 -    0.141: 154
       0.141 -    0.211: 12
       0.211 -    0.281: 2
       0.281 -    0.352: 3
  Chirality restraints: 1477
  Sorted by residual:
  chirality pdb=" CG  LEU A  84 "
            pdb=" CB  LEU A  84 "
            pdb=" CD1 LEU A  84 "
            pdb=" CD2 LEU A  84 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.24   -0.35 2.00e-01 2.50e+01 3.09e+00
  chirality pdb=" C3'   G B  95 "
            pdb=" C4'   G B  95 "
            pdb=" O3'   G B  95 "
            pdb=" C2'   G B  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.42   -0.32 2.00e-01 2.50e+01 2.61e+00
  chirality pdb=" C3'   A B  12 "
            pdb=" C4'   A B  12 "
            pdb=" O3'   A B  12 "
            pdb=" C2'   A B  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.18   -0.29 2.00e-01 2.50e+01 2.16e+00
  ... (remaining 1474 not shown)

  Planarity restraints: 1187
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A   9 "    0.081 5.00e-02 4.00e+02   1.24e-01 2.47e+01
        pdb=" N   PRO A  10 "   -0.215 5.00e-02 4.00e+02
        pdb=" CA  PRO A  10 "    0.068 5.00e-02 4.00e+02
        pdb=" CD  PRO A  10 "    0.066 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  14 "    0.217 9.50e-02 1.11e+02   9.78e-02 6.63e+00
        pdb=" NE  ARG A  14 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  14 "   -0.018 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  14 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  14 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B  97 "    0.027 2.00e-02 2.50e+03   1.39e-02 5.84e+00
        pdb=" N9    G B  97 "   -0.024 2.00e-02 2.50e+03
        pdb=" C8    G B  97 "   -0.026 2.00e-02 2.50e+03
        pdb=" N7    G B  97 "    0.006 2.00e-02 2.50e+03
        pdb=" C5    G B  97 "    0.007 2.00e-02 2.50e+03
        pdb=" C6    G B  97 "    0.004 2.00e-02 2.50e+03
        pdb=" O6    G B  97 "    0.005 2.00e-02 2.50e+03
        pdb=" N1    G B  97 "    0.001 2.00e-02 2.50e+03
        pdb=" C2    G B  97 "   -0.004 2.00e-02 2.50e+03
        pdb=" N2    G B  97 "   -0.009 2.00e-02 2.50e+03
        pdb=" N3    G B  97 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4    G B  97 "    0.013 2.00e-02 2.50e+03
  ... (remaining 1184 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 460
        2.72 -     3.26: 7425
        3.26 -     3.81: 16411
        3.81 -     4.35: 19740
        4.35 -     4.90: 29586
  Nonbonded interactions: 73622
  Sorted by model distance:
  nonbonded pdb=" ND1 HIS A 750 "
            pdb="MG    MG A1201 "
     model   vdw
     2.174 2.250
  nonbonded pdb=" OG1 THR A 504 "
            pdb=" OH  TYR A 698 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" OG  SER A  59 "
            pdb=" OP1   C B  17 "
     model   vdw
     2.306 3.040
  nonbonded pdb=" O   LEU A 842 "
            pdb=" O2'   C B  26 "
     model   vdw
     2.320 3.040
  nonbonded pdb=" O2'   A B  40 "
            pdb=" O4'   A B  41 "
     model   vdw
     2.321 3.040
  ... (remaining 73617 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.760
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     11.130
  Find NCS groups from input model:        0.030
  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:             0.000
  Load rotamer database and sin/cos tables:7.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.078   8903  Z= 0.212
  Angle     :  0.850  10.801  12655  Z= 0.445
  Chirality :  0.048   0.352   1477
  Planarity :  0.009   0.124   1187
  Dihedral  : 21.022 170.963   3975
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.38 %
    Cis-general     : 0.29 %
    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: -1.19 (0.27), residues: 739
  helix: -0.38 (0.26), residues: 322
  sheet: -0.23 (0.54), residues: 83
  loop : -1.26 (0.28), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A  14 
 TYR   0.014   0.003   TYR A 986 
 PHE   0.016   0.002   PHE A  76 
 TRP   0.021   0.002   TRP A1128 
 HIS   0.012   0.002   HIS A 749 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 ( 8903)
  covalent geometry    : angle       0.84982 (12655)
  hydrogen bonds       : bond        0.07399 (  380)
  hydrogen bonds       : angle       5.16348 ( 1005)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.239 
Fit side-chains
REVERT: A   86 MET cc_start: 0.7800 (mtt) cc_final: 0.7579 (mtp)
REVERT: A   98 ASP cc_start: 0.7976 (m-30) cc_final: 0.7645 (m-30)
REVERT: A  125 ARG cc_start: 0.7287 (mtp85) cc_final: 0.7056 (mtp180)
REVERT: A 1025 ASP cc_start: 0.7204 (m-30) cc_final: 0.6889 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.8471
  time to fit residues: 56.7591
Evaluate side-chains
  42 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:   10.0000
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    5.9990
   chunk 74 optimal weight:    7.9990
   overall best weight:    1.8786

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

Flipped N/Q/H residues before XYZ refinement:
** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.176671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.137644 restraints weight = 8974.701|
|-----------------------------------------------------------------------------|
r_work (start): 0.3564 rms_B_bonded: 1.36
r_work: 0.3313 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3187 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.1227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8903  Z= 0.206
  Angle     :  0.614   6.619  12655  Z= 0.323
  Chirality :  0.041   0.213   1477
  Planarity :  0.006   0.077   1187
  Dihedral  : 22.400 158.145   2597
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  :  6.92 %
    Favored  : 91.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.38 %
    Cis-general     : 0.29 %
    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 (0.29), residues: 739
  helix:  0.94 (0.29), residues: 326
  sheet: -0.07 (0.55), residues: 83
  loop : -0.93 (0.28), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 137 
 TYR   0.019   0.002   TYR A 986 
 PHE   0.007   0.001   PHE A  76 
 TRP   0.012   0.002   TRP A1128 
 HIS   0.005   0.001   HIS A 936 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 ( 8903)
  covalent geometry    : angle       0.61352 (12655)
  hydrogen bonds       : bond        0.05390 (  380)
  hydrogen bonds       : angle       4.22826 ( 1005)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 53
  time to evaluate  : 0.201 
Fit side-chains
REVERT: A  125 ARG cc_start: 0.7499 (mtp85) cc_final: 0.7103 (mtm180)
REVERT: A  162 GLU cc_start: 0.6497 (OUTLIER) cc_final: 0.6277 (mt-10)
REVERT: A  815 ILE cc_start: 0.7999 (OUTLIER) cc_final: 0.7743 (mp)
REVERT: A  904 ARG cc_start: 0.6833 (OUTLIER) cc_final: 0.6296 (ptt-90)
REVERT: A 1028 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.6940 (mmp)
  outliers start: 12
  outliers final: 4
  residues processed: 57
  average time/residue: 0.8405
  time to fit residues: 50.2305
Evaluate side-chains
  51 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 43
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 GLU
Chi-restraints excluded: chain A residue  218 THR
Chi-restraints excluded: chain A residue  815 ILE
Chi-restraints excluded: chain A residue  900 VAL
Chi-restraints excluded: chain A residue  904 ARG
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain A residue 1028 MET
Chi-restraints excluded: chain A residue 1118 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 80 optimal weight:    4.9990
   chunk 2 optimal weight:    7.9990
   chunk 82 optimal weight:    5.9990
   chunk 54 optimal weight:    5.9990
   chunk 18 optimal weight:    4.9990
   chunk 40 optimal weight:    0.0770
   chunk 9 optimal weight:    2.9990
   chunk 16 optimal weight:    6.9990
   chunk 29 optimal weight:    9.9990
   chunk 67 optimal weight:    6.9990
   chunk 61 optimal weight:    5.9990
   overall best weight:    3.8146

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

Flipped N/Q/H residues before XYZ refinement:
** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 486 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.172369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.132020 restraints weight = 8945.525|
|-----------------------------------------------------------------------------|
r_work (start): 0.3497 rms_B_bonded: 1.44
r_work: 0.3258 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3133 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8379
moved from start:          0.1982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.074   8903  Z= 0.351
  Angle     :  0.743   9.684  12655  Z= 0.388
  Chirality :  0.048   0.233   1477
  Planarity :  0.008   0.106   1187
  Dihedral  : 22.543 154.974   2597
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  :  9.56 %
    Favored  : 87.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.38 %
    Cis-general     : 0.29 %
    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: -0.10 (0.28), residues: 739
  helix:  0.89 (0.28), residues: 331
  sheet: -0.35 (0.53), residues: 83
  loop : -0.95 (0.29), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 137 
 TYR   0.024   0.003   TYR A 986 
 PHE   0.010   0.002   PHE A 881 
 TRP   0.013   0.002   TRP A 854 
 HIS   0.007   0.002   HIS A 936 

Details of bonding type rmsd
  covalent geometry    : bond        0.00769 ( 8903)
  covalent geometry    : angle       0.74288 (12655)
  hydrogen bonds       : bond        0.06534 (  380)
  hydrogen bonds       : angle       4.29057 ( 1005)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 43
  time to evaluate  : 0.251 
Fit side-chains
REVERT: A   14 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8018 (mtm-85)
REVERT: A  125 ARG cc_start: 0.7644 (mtp85) cc_final: 0.7151 (mtp180)
REVERT: A  804 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.7109 (mtpm)
REVERT: A  815 ILE cc_start: 0.8066 (OUTLIER) cc_final: 0.7727 (mp)
REVERT: A  976 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7649 (mp0)
  outliers start: 20
  outliers final: 9
  residues processed: 57
  average time/residue: 0.7718
  time to fit residues: 46.2606
Evaluate side-chains
  56 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 43
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   14 ARG
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  758 THR
Chi-restraints excluded: chain A residue  804 LYS
Chi-restraints excluded: chain A residue  815 ILE
Chi-restraints excluded: chain A residue  900 VAL
Chi-restraints excluded: chain A residue  904 ARG
Chi-restraints excluded: chain A residue  976 GLU
Chi-restraints excluded: chain A residue  989 ILE
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain A residue 1118 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 14 optimal weight:    8.9990
   chunk 45 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 30 optimal weight:    4.9990
   chunk 21 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 74 optimal weight:    6.9990
   chunk 58 optimal weight:    0.9990
   chunk 39 optimal weight:    3.9990
   overall best weight:    1.7388

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

Flipped N/Q/H residues before XYZ refinement:
** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 486 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.174924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.135775 restraints weight = 9090.132|
|-----------------------------------------------------------------------------|
r_work (start): 0.3541 rms_B_bonded: 1.39
r_work: 0.3291 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3167 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8336
moved from start:          0.1872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8903  Z= 0.196
  Angle     :  0.602   7.093  12655  Z= 0.318
  Chirality :  0.041   0.228   1477
  Planarity :  0.005   0.073   1187
  Dihedral  : 22.344 155.425   2597
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 13.34 %
    Favored  : 84.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.38 %
    Cis-general     : 0.29 %
    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:  0.26 (0.29), residues: 739
  helix:  1.27 (0.29), residues: 329
  sheet: -0.46 (0.53), residues: 83
  loop : -0.75 (0.30), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A1048 
 TYR   0.018   0.002   TYR A 986 
 PHE   0.008   0.001   PHE A 730 
 TRP   0.010   0.002   TRP A 854 
 HIS   0.004   0.001   HIS A 936 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 ( 8903)
  covalent geometry    : angle       0.60182 (12655)
  hydrogen bonds       : bond        0.05233 (  380)
  hydrogen bonds       : angle       4.02869 ( 1005)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 51
  time to evaluate  : 0.197 
Fit side-chains
REVERT: A   14 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8057 (mtm-85)
REVERT: A  125 ARG cc_start: 0.7516 (mtp85) cc_final: 0.7081 (mtp180)
REVERT: A  815 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7721 (mp)
REVERT: A  904 ARG cc_start: 0.6936 (OUTLIER) cc_final: 0.6659 (ptt-90)
REVERT: A 1028 MET cc_start: 0.7746 (ptt) cc_final: 0.6943 (mmp)
  outliers start: 11
  outliers final: 3
  residues processed: 58
  average time/residue: 0.8833
  time to fit residues: 53.4978
Evaluate side-chains
  54 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 48
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   14 ARG
Chi-restraints excluded: chain A residue  815 ILE
Chi-restraints excluded: chain A residue  904 ARG
Chi-restraints excluded: chain A residue  989 ILE
Chi-restraints excluded: chain A residue 1118 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 46 optimal weight:    6.9990
   chunk 69 optimal weight:    9.9990
   chunk 53 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 43 optimal weight:    4.9990
   chunk 22 optimal weight:    7.9990
   chunk 34 optimal weight:    5.9990
   chunk 6 optimal weight:    3.9990
   chunk 19 optimal weight:    6.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 486 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.173954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.133831 restraints weight = 9105.490|
|-----------------------------------------------------------------------------|
r_work (start): 0.3511 rms_B_bonded: 1.37
r_work: 0.3272 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3150 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
moved from start:          0.1981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   8903  Z= 0.229
  Angle     :  0.633   8.890  12655  Z= 0.332
  Chirality :  0.042   0.220   1477
  Planarity :  0.006   0.078   1187
  Dihedral  : 22.341 155.405   2597
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 12.69 %
    Favored  : 83.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.38 %
    Cis-general     : 0.29 %
    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:  0.26 (0.29), residues: 739
  helix:  1.30 (0.29), residues: 330
  sheet: -0.60 (0.53), residues: 83
  loop : -0.75 (0.30), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A1048 
 TYR   0.020   0.002   TYR A 986 
 PHE   0.008   0.001   PHE A 730 
 TRP   0.009   0.002   TRP A 854 
 HIS   0.005   0.001   HIS A 936 

Details of bonding type rmsd
  covalent geometry    : bond        0.00498 ( 8903)
  covalent geometry    : angle       0.63324 (12655)
  hydrogen bonds       : bond        0.05545 (  380)
  hydrogen bonds       : angle       4.00608 ( 1005)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 51
  time to evaluate  : 0.264 
Fit side-chains
REVERT: A   14 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.8038 (mtm-85)
REVERT: A  482 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7061 (mt-10)
REVERT: A  684 THR cc_start: 0.5185 (OUTLIER) cc_final: 0.4976 (m)
REVERT: A  692 ARG cc_start: 0.7630 (ttp80) cc_final: 0.7300 (ttp80)
REVERT: A  804 LYS cc_start: 0.7421 (OUTLIER) cc_final: 0.7140 (mtpm)
REVERT: A  815 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7716 (mp)
REVERT: A 1028 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.6904 (mmp)
  outliers start: 22
  outliers final: 9
  residues processed: 66
  average time/residue: 0.8341
  time to fit residues: 57.6344
Evaluate side-chains
  60 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 45
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   14 ARG
Chi-restraints excluded: chain A residue  482 GLU
Chi-restraints excluded: chain A residue  684 THR
Chi-restraints excluded: chain A residue  706 GLN
Chi-restraints excluded: chain A residue  758 THR
Chi-restraints excluded: chain A residue  804 LYS
Chi-restraints excluded: chain A residue  815 ILE
Chi-restraints excluded: chain A residue  900 VAL
Chi-restraints excluded: chain A residue  904 ARG
Chi-restraints excluded: chain A residue  989 ILE
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain A residue 1028 MET
Chi-restraints excluded: chain A residue 1118 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 79 optimal weight:    9.9990
   chunk 57 optimal weight:    4.9990
   chunk 30 optimal weight:   10.0000
   chunk 43 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 21 optimal weight:    5.9990
   chunk 45 optimal weight:    3.9990
   chunk 19 optimal weight:    6.9990
   chunk 71 optimal weight:    2.9990
   chunk 37 optimal weight:    9.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 486 HIS
A1060 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.172248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.132369 restraints weight = 8915.531|
|-----------------------------------------------------------------------------|
r_work (start): 0.3498 rms_B_bonded: 1.50
r_work: 0.3243 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3120 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
moved from start:          0.2213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.059   8903  Z= 0.300
  Angle     :  0.697   7.785  12655  Z= 0.364
  Chirality :  0.046   0.227   1477
  Planarity :  0.006   0.057   1187
  Dihedral  : 22.413 154.280   2597
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 14.17 %
    Favored  : 82.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.38 %
    Cis-general     : 0.29 %
    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:  0.06 (0.29), residues: 739
  helix:  1.08 (0.28), residues: 331
  sheet: -0.71 (0.53), residues: 83
  loop : -0.79 (0.30), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A1048 
 TYR   0.023   0.003   TYR A 986 
 PHE   0.010   0.002   PHE A 730 
 TRP   0.011   0.002   TRP A 854 
 HIS   0.006   0.002   HIS A 936 

Details of bonding type rmsd
  covalent geometry    : bond        0.00654 ( 8903)
  covalent geometry    : angle       0.69704 (12655)
  hydrogen bonds       : bond        0.06106 (  380)
  hydrogen bonds       : angle       4.10522 ( 1005)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 48
  time to evaluate  : 0.166 
Fit side-chains
REVERT: A   14 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7996 (mtm-85)
REVERT: A  125 ARG cc_start: 0.7555 (mtt180) cc_final: 0.7104 (mtm180)
REVERT: A  684 THR cc_start: 0.5122 (OUTLIER) cc_final: 0.4753 (p)
REVERT: A  692 ARG cc_start: 0.7736 (ttp80) cc_final: 0.7464 (ttp80)
REVERT: A  804 LYS cc_start: 0.7453 (OUTLIER) cc_final: 0.7147 (mtpm)
REVERT: A  815 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7716 (mp)
REVERT: A  976 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7684 (mp0)
REVERT: A 1028 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.6921 (mmp)
REVERT: A 1064 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.6931 (mp)
  outliers start: 20
  outliers final: 11
  residues processed: 61
  average time/residue: 0.7773
  time to fit residues: 49.5714
Evaluate side-chains
  63 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 45
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   14 ARG
Chi-restraints excluded: chain A residue  150 ASP
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  684 THR
Chi-restraints excluded: chain A residue  706 GLN
Chi-restraints excluded: chain A residue  758 THR
Chi-restraints excluded: chain A residue  804 LYS
Chi-restraints excluded: chain A residue  815 ILE
Chi-restraints excluded: chain A residue  900 VAL
Chi-restraints excluded: chain A residue  904 ARG
Chi-restraints excluded: chain A residue  976 GLU
Chi-restraints excluded: chain A residue  989 ILE
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain A residue 1028 MET
Chi-restraints excluded: chain A residue 1064 LEU
Chi-restraints excluded: chain A residue 1118 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 75 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   chunk 3 optimal weight:    0.6980
   chunk 46 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 42 optimal weight:    5.9990
   chunk 82 optimal weight:    4.9990
   chunk 65 optimal weight:    0.6980
   chunk 63 optimal weight:    0.8980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 486 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.177789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.138849 restraints weight = 9196.851|
|-----------------------------------------------------------------------------|
r_work (start): 0.3582 rms_B_bonded: 1.37
r_work: 0.3349 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3229 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.1994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8903  Z= 0.148
  Angle     :  0.567   7.512  12655  Z= 0.300
  Chirality :  0.039   0.235   1477
  Planarity :  0.005   0.066   1187
  Dihedral  : 22.238 155.898   2597
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 15.65 %
    Favored  : 82.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.38 %
    Cis-general     : 0.29 %
    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:  0.46 (0.30), residues: 739
  helix:  1.52 (0.29), residues: 329
  sheet: -0.66 (0.53), residues: 85
  loop : -0.64 (0.31), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG A1048 
 TYR   0.016   0.002   TYR A 698 
 PHE   0.007   0.001   PHE A 730 
 TRP   0.008   0.001   TRP A 854 
 HIS   0.004   0.001   HIS A 486 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 8903)
  covalent geometry    : angle       0.56685 (12655)
  hydrogen bonds       : bond        0.04900 (  380)
  hydrogen bonds       : angle       3.88648 ( 1005)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 51
  time to evaluate  : 0.265 
Fit side-chains
REVERT: A   14 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.8089 (mtm-85)
REVERT: A  684 THR cc_start: 0.5551 (OUTLIER) cc_final: 0.5189 (p)
REVERT: A  692 ARG cc_start: 0.7656 (ttp80) cc_final: 0.7359 (ttp80)
REVERT: A  815 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7702 (mp)
REVERT: A 1028 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.6903 (mmp)
REVERT: A 1064 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.6885 (mp)
  outliers start: 13
  outliers final: 6
  residues processed: 60
  average time/residue: 0.8289
  time to fit residues: 52.1956
Evaluate side-chains
  61 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 50
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   14 ARG
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  684 THR
Chi-restraints excluded: chain A residue  706 GLN
Chi-restraints excluded: chain A residue  758 THR
Chi-restraints excluded: chain A residue  815 ILE
Chi-restraints excluded: chain A residue  989 ILE
Chi-restraints excluded: chain A residue 1028 MET
Chi-restraints excluded: chain A residue 1064 LEU
Chi-restraints excluded: chain A residue 1118 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 37 optimal weight:    7.9990
   chunk 79 optimal weight:   10.0000
   chunk 39 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   chunk 29 optimal weight:    0.4980
   chunk 74 optimal weight:    8.9990
   chunk 17 optimal weight:    0.7980
   chunk 42 optimal weight:    4.9990
   chunk 75 optimal weight:    4.9990
   chunk 30 optimal weight:   10.0000
   chunk 73 optimal weight:    5.9990
   overall best weight:    1.5982

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

Flipped N/Q/H residues before XYZ refinement:
A 486 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.176362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.137570 restraints weight = 9078.479|
|-----------------------------------------------------------------------------|
r_work (start): 0.3566 rms_B_bonded: 1.39
r_work: 0.3325 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3204 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start:          0.2045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8903  Z= 0.185
  Angle     :  0.590   9.676  12655  Z= 0.312
  Chirality :  0.040   0.224   1477
  Planarity :  0.006   0.093   1187
  Dihedral  : 22.235 155.474   2597
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 16.14 %
    Favored  : 81.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.38 %
    Cis-general     : 0.29 %
    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:  0.48 (0.30), residues: 739
  helix:  1.53 (0.29), residues: 329
  sheet: -0.66 (0.53), residues: 85
  loop : -0.63 (0.31), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A1048 
 TYR   0.020   0.002   TYR A 698 
 PHE   0.007   0.001   PHE A 730 
 TRP   0.007   0.001   TRP A 141 
 HIS   0.004   0.001   HIS A 486 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 ( 8903)
  covalent geometry    : angle       0.59000 (12655)
  hydrogen bonds       : bond        0.05184 (  380)
  hydrogen bonds       : angle       3.89025 ( 1005)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 51
  time to evaluate  : 0.267 
Fit side-chains
REVERT: A   14 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.8046 (mtm-85)
REVERT: A  125 ARG cc_start: 0.7454 (mtt180) cc_final: 0.7055 (mtp180)
REVERT: A  162 GLU cc_start: 0.6596 (OUTLIER) cc_final: 0.6323 (mt-10)
REVERT: A  684 THR cc_start: 0.5444 (OUTLIER) cc_final: 0.5075 (p)
REVERT: A  692 ARG cc_start: 0.7678 (ttp80) cc_final: 0.7422 (ttp80)
REVERT: A  693 ASP cc_start: 0.7145 (m-30) cc_final: 0.6896 (m-30)
REVERT: A  815 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7755 (mp)
REVERT: A 1028 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.6911 (mmp)
REVERT: A 1064 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.6925 (mp)
  outliers start: 15
  outliers final: 8
  residues processed: 62
  average time/residue: 0.7660
  time to fit residues: 49.9725
Evaluate side-chains
  63 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 49
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   14 ARG
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue  162 GLU
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  684 THR
Chi-restraints excluded: chain A residue  706 GLN
Chi-restraints excluded: chain A residue  758 THR
Chi-restraints excluded: chain A residue  815 ILE
Chi-restraints excluded: chain A residue  989 ILE
Chi-restraints excluded: chain A residue 1028 MET
Chi-restraints excluded: chain A residue 1064 LEU
Chi-restraints excluded: chain A residue 1118 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 68 optimal weight:    0.1980
   chunk 39 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 81 optimal weight:    9.9990
   chunk 2 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   chunk 82 optimal weight:    5.9990
   chunk 79 optimal weight:    9.9990
   chunk 38 optimal weight:    0.9980
   chunk 57 optimal weight:    4.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 190 GLN
A 486 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.178229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.138747 restraints weight = 9067.025|
|-----------------------------------------------------------------------------|
r_work (start): 0.3580 rms_B_bonded: 1.27
r_work: 0.3360 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3238 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8282
moved from start:          0.1973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   8903  Z= 0.147
  Angle     :  0.549   7.057  12655  Z= 0.292
  Chirality :  0.038   0.231   1477
  Planarity :  0.004   0.052   1187
  Dihedral  : 22.175 156.090   2597
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 16.14 %
    Favored  : 81.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.38 %
    Cis-general     : 0.29 %
    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:  0.65 (0.30), residues: 739
  helix:  1.67 (0.29), residues: 329
  sheet: -0.60 (0.53), residues: 85
  loop : -0.52 (0.31), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1048 
 TYR   0.019   0.002   TYR A 698 
 PHE   0.007   0.001   PHE A 730 
 TRP   0.008   0.001   TRP A 161 
 HIS   0.004   0.001   HIS A 486 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 8903)
  covalent geometry    : angle       0.54930 (12655)
  hydrogen bonds       : bond        0.04878 (  380)
  hydrogen bonds       : angle       3.81741 ( 1005)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 50
  time to evaluate  : 0.254 
Fit side-chains
REVERT: A   14 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8071 (mtm-85)
REVERT: A  162 GLU cc_start: 0.6513 (OUTLIER) cc_final: 0.6232 (mt-10)
REVERT: A  190 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7664 (mm110)
REVERT: A  684 THR cc_start: 0.5597 (OUTLIER) cc_final: 0.5252 (p)
REVERT: A  692 ARG cc_start: 0.7622 (ttp80) cc_final: 0.7321 (ttp80)
REVERT: A  693 ASP cc_start: 0.7088 (m-30) cc_final: 0.6852 (m-30)
REVERT: A  815 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7714 (mp)
REVERT: A 1028 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.6845 (mmp)
REVERT: A 1064 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.6915 (mp)
  outliers start: 15
  outliers final: 7
  residues processed: 61
  average time/residue: 0.8174
  time to fit residues: 52.3641
Evaluate side-chains
  63 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 49
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   14 ARG
Chi-restraints excluded: chain A residue  162 GLU
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  190 GLN
Chi-restraints excluded: chain A residue  684 THR
Chi-restraints excluded: chain A residue  706 GLN
Chi-restraints excluded: chain A residue  758 THR
Chi-restraints excluded: chain A residue  815 ILE
Chi-restraints excluded: chain A residue  989 ILE
Chi-restraints excluded: chain A residue 1028 MET
Chi-restraints excluded: chain A residue 1064 LEU
Chi-restraints excluded: chain A residue 1118 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 73 optimal weight:    4.9990
   chunk 40 optimal weight:    0.0970
   chunk 29 optimal weight:    0.3980
   chunk 77 optimal weight:    8.9990
   chunk 27 optimal weight:    5.9990
   chunk 83 optimal weight:    5.9990
   chunk 62 optimal weight:    0.8980
   chunk 4 optimal weight:    9.9990
   chunk 18 optimal weight:    0.9980
   chunk 33 optimal weight:    5.9990
   chunk 21 optimal weight:    6.9990
   overall best weight:    1.4780

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

Flipped N/Q/H residues before XYZ refinement:
A 486 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.176969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.138314 restraints weight = 9086.706|
|-----------------------------------------------------------------------------|
r_work (start): 0.3575 rms_B_bonded: 1.36
r_work: 0.3333 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3211 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
moved from start:          0.2012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8903  Z= 0.174
  Angle     :  0.572   7.116  12655  Z= 0.303
  Chirality :  0.040   0.222   1477
  Planarity :  0.005   0.055   1187
  Dihedral  : 22.190 155.610   2597
  Min Nonbonded Distance : 2.072

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 16.80 %
    Favored  : 80.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.38 %
    Cis-general     : 0.29 %
    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:  0.61 (0.30), residues: 739
  helix:  1.63 (0.29), residues: 330
  sheet: -0.57 (0.53), residues: 85
  loop : -0.56 (0.31), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A1048 
 TYR   0.020   0.002   TYR A 698 
 PHE   0.008   0.001   PHE A 730 
 TRP   0.007   0.001   TRP A 161 
 HIS   0.003   0.001   HIS A 486 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 8903)
  covalent geometry    : angle       0.57218 (12655)
  hydrogen bonds       : bond        0.04936 (  380)
  hydrogen bonds       : angle       3.82068 ( 1005)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 50
  time to evaluate  : 0.246 
Fit side-chains
REVERT: A   14 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.8102 (mtm-85)
REVERT: A  162 GLU cc_start: 0.6584 (OUTLIER) cc_final: 0.6308 (mt-10)
REVERT: A  684 THR cc_start: 0.5526 (OUTLIER) cc_final: 0.5171 (p)
REVERT: A  692 ARG cc_start: 0.7680 (ttp80) cc_final: 0.7393 (ttp80)
REVERT: A  693 ASP cc_start: 0.7114 (m-30) cc_final: 0.6878 (m-30)
REVERT: A  815 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7748 (mp)
REVERT: A 1028 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.6919 (mmp)
REVERT: A 1064 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.6975 (mp)
  outliers start: 14
  outliers final: 7
  residues processed: 60
  average time/residue: 0.8286
  time to fit residues: 52.1969
Evaluate side-chains
  63 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 50
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   14 ARG
Chi-restraints excluded: chain A residue  162 GLU
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  684 THR
Chi-restraints excluded: chain A residue  706 GLN
Chi-restraints excluded: chain A residue  758 THR
Chi-restraints excluded: chain A residue  815 ILE
Chi-restraints excluded: chain A residue  989 ILE
Chi-restraints excluded: chain A residue 1028 MET
Chi-restraints excluded: chain A residue 1064 LEU
Chi-restraints excluded: chain A residue 1118 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 53 optimal weight:    0.7980
   chunk 74 optimal weight:    7.9990
   chunk 39 optimal weight:    2.9990
   chunk 0 optimal weight:    8.9990
   chunk 41 optimal weight:    0.0050
   chunk 19 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 60 optimal weight:    0.6980
   chunk 80 optimal weight:    4.9990
   chunk 30 optimal weight:    9.9990
   chunk 32 optimal weight:    5.9990
   overall best weight:    0.8396

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

Flipped N/Q/H residues before XYZ refinement:
** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 486 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.177945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.138395 restraints weight = 9103.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.3577 rms_B_bonded: 1.47
r_work: 0.3338 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3216 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
moved from start:          0.1995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8903  Z= 0.139
  Angle     :  0.554   7.722  12655  Z= 0.294
  Chirality :  0.038   0.232   1477
  Planarity :  0.005   0.094   1187
  Dihedral  : 22.182 155.744   2597
  Min Nonbonded Distance : 2.072

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 17.30 %
    Favored  : 80.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.38 %
    Cis-general     : 0.29 %
    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:  0.66 (0.30), residues: 739
  helix:  1.66 (0.29), residues: 330
  sheet: -0.56 (0.54), residues: 85
  loop : -0.51 (0.31), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A1048 
 TYR   0.019   0.002   TYR A 698 
 PHE   0.008   0.001   PHE A 730 
 TRP   0.007   0.001   TRP A 141 
 HIS   0.005   0.001   HIS A 486 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 8903)
  covalent geometry    : angle       0.55394 (12655)
  hydrogen bonds       : bond        0.04797 (  380)
  hydrogen bonds       : angle       3.80513 ( 1005)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3210.47 seconds
wall clock time: 55 minutes 15.76 seconds (3315.76 seconds total)