Starting phenix.real_space_refine
on Wed Jul 30 04:14:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vyo_43673/07_2025/8vyo_43673.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vyo_43673/07_2025/8vyo_43673.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.74
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vyo_43673/07_2025/8vyo_43673.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vyo_43673/07_2025/8vyo_43673.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vyo_43673/07_2025/8vyo_43673.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vyo_43673/07_2025/8vyo_43673.cif"
  }
  resolution = 3.74
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.039
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: 7
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P       2      5.49       5
     S      34      5.16       5
     C    3818      2.51       5
     N    1038      2.21       5
     O    1142      1.98       5
     H    6039      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12075
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5009
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 309, 5009
          Classifications: {'peptide': 309}
          Link IDs: {'PTRANS': 13, 'TRANS': 295}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 3589
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 3589
          Classifications: {'peptide': 223}
          Modifications used: {'NH1NOTPRO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 218}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 3475
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 3475
          Classifications: {'peptide': 218}
          Modifications used: {'NH1NOTPRO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 213}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    236  SG  CYS A 248      50.472  42.917  50.745  1.00 89.46           S
  ATOM    279  SG  CYS A 251      51.735  43.151  47.111  1.00 97.16           S
  ATOM    462  SG  CYS A 261      46.788  48.902  61.308  1.00 94.52           S
  ATOM    504  SG  CYS A 264      45.432  51.693  60.944  1.00 97.46           S

  Time building chain proxies: 6.05, per 1000 atoms: 0.50
  Number of scatterers: 12075
  At special positions: 0
  Unit cell: (75.9, 89.1, 103.95, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      2     29.99
     S      34     16.00
     P       2     15.00
     O    1142      8.00
     N    1038      7.00
     C    3818      6.00
     H    6039      1.00
    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: 3.51
  Conformation dependent library (CDL) restraints added in 929.2 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 901 "
        pdb="ZN    ZN A 901 " - pdb=" ND1 HIS A 269 "
        pdb="ZN    ZN A 901 " - pdb=" SG  CYS A 248 "
        pdb="ZN    ZN A 901 " - pdb=" SG  CYS A 251 "
      pdb="  ZN A 902 "
        pdb="ZN    ZN A 902 " - pdb=" SG  CYS A 261 "
        pdb="ZN    ZN A 902 " - pdb=" SG  CYS A 264 "
        pdb="ZN    ZN A 902 " - pdb=" ND1 HIS A 235 "


  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1440

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 3 sheets defined
      69.5% alpha, 3.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.05
  Creating SS restraints...
    Processing helix  chain 'A' and resid 491 through 506
    Processing helix  chain 'A' and resid 536 through 543
      removed outlier: 3.640A  pdb=" N   HIS A 540 " --> pdb=" O   SER A 536 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 549 through 570
    Processing helix  chain 'A' and resid 578 through 580
      No H-bonds generated for 'chain 'A' and resid 578 through 580'
    Processing helix  chain 'A' and resid 597 through 601
    Processing helix  chain 'A' and resid 621 through 626
    Processing helix  chain 'A' and resid 636 through 652
      removed outlier: 3.510A  pdb=" N   TYR A 640 " --> pdb=" O   GLN A 636 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 661 through 671
      removed outlier: 4.629A  pdb=" N   PHE A 667 " --> pdb=" O   ASP A 663 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   MET A 668 " --> pdb=" O   GLN A 664 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 677 through 681
      removed outlier: 3.730A  pdb=" N   VAL A 681 " --> pdb=" O   LEU A 678 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 697
    Processing helix  chain 'A' and resid 700 through 704
      removed outlier: 3.761A  pdb=" N   GLU A 703 " --> pdb=" O   LYS A 700 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 706 through 724
      removed outlier: 3.632A  pdb=" N   ARG A 719 " --> pdb=" O   GLU A 715 " (cutoff:3.500A)
      Proline residue:  A 722  - end of helix
    Processing helix  chain 'B' and resid 3 through 16
      removed outlier: 3.593A  pdb=" N   GLN B  15 " --> pdb=" O   LYS B  11 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 18 through 32
      removed outlier: 3.918A  pdb=" N   ALA B  24 " --> pdb=" O   ASP B  20 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   GLN B  32 " --> pdb=" O   SER B  28 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 37 through 66
      removed outlier: 4.254A  pdb=" N   ARG B  55 " --> pdb=" O   VAL B  51 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 73 through 105
      removed outlier: 3.595A  pdb=" N   LEU B 105 " --> pdb=" O   LEU B 101 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 106 through 109
    Processing helix  chain 'B' and resid 111 through 133
      removed outlier: 3.511A  pdb=" N   LYS B 115 " --> pdb=" O   GLN B 111 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   VAL B 116 " --> pdb=" O   ALA B 112 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 160
      removed outlier: 4.289A  pdb=" N   LYS B 158 " --> pdb=" O   GLU B 154 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   MET B 160 " --> pdb=" O   SER B 156 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 181
    Processing helix  chain 'B' and resid 184 through 202
      removed outlier: 3.523A  pdb=" N   ALA B 188 " --> pdb=" O   SER B 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 230
    Processing helix  chain 'C' and resid 3 through 16
      removed outlier: 3.711A  pdb=" N   GLN C  15 " --> pdb=" O   LYS C  11 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 18 through 31
      removed outlier: 3.862A  pdb=" N   SER C  28 " --> pdb=" O   ALA C  24 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   VAL C  29 " --> pdb=" O   CYS C  25 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   THR C  30 " --> pdb=" O   MET C  26 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 37 through 68
      removed outlier: 3.999A  pdb=" N   ASN C  42 " --> pdb=" O   ASN C  38 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   ARG C  55 " --> pdb=" O   VAL C  51 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 74 through 104
      removed outlier: 4.228A  pdb=" N   MET C  78 " --> pdb=" O   LYS C  74 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 113 through 133
      removed outlier: 3.625A  pdb=" N   LEU C 119 " --> pdb=" O   LYS C 115 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 134 through 152
      removed outlier: 4.002A  pdb=" N   LYS C 139 " --> pdb=" O   GLY C 135 " (cutoff:3.500A)
      removed outlier: 4.201A  pdb=" N   GLY C 140 " --> pdb=" O   ASP C 136 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   GLN C 144 " --> pdb=" O   GLY C 140 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 164 through 181
    Processing helix  chain 'C' and resid 184 through 201
    Processing helix  chain 'C' and resid 205 through 210
    Processing helix  chain 'C' and resid 210 through 229
      removed outlier: 3.742A  pdb=" N   SER C 214 " --> pdb=" O   SER C 210 " (cutoff:3.500A)
      removed outlier: 4.787A  pdb=" N   LEU C 216 " --> pdb=" O   LYS C 212 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 237 through 241
    Processing sheet with id=AA2, first strand: chain 'A' and resid 462 through 464
      removed outlier: 7.083A  pdb=" N   GLN A 530 " --> pdb=" O   PHE A 516 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   PHE A 516 " --> pdb=" O   GLN A 530 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 582 through 584

    383 hydrogen bonds defined for protein.
    1134 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.98

  Time building geometry restraints manager: 4.20 seconds

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

  Histogram of bond lengths:
        0.83 -     1.03: 6026
        1.03 -     1.23: 25
        1.23 -     1.42: 2537
        1.42 -     1.62: 3531
        1.62 -     1.82: 55
  Bond restraints: 12174
  Sorted by residual:
  bond pdb=" N   ASP B   2 "
       pdb=" H1  ASP B   2 "
    ideal  model  delta    sigma   weight residual
    0.960  0.861  0.099 2.00e-02 2.50e+03 2.47e+01
  bond pdb=" N   ASP C   2 "
       pdb=" H1  ASP C   2 "
    ideal  model  delta    sigma   weight residual
    0.960  0.861  0.099 2.00e-02 2.50e+03 2.44e+01
  bond pdb=" N   ASN B   4 "
       pdb=" H   ASN B   4 "
    ideal  model  delta    sigma   weight residual
    0.860  0.912 -0.052 2.00e-02 2.50e+03 6.69e+00
  bond pdb=" N   LEU B   6 "
       pdb=" H   LEU B   6 "
    ideal  model  delta    sigma   weight residual
    0.860  0.911 -0.051 2.00e-02 2.50e+03 6.50e+00
  bond pdb=" N   LEU B   6 "
       pdb=" CA  LEU B   6 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.23e-02 6.61e+03 5.65e+00
  ... (remaining 12169 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.52: 21264
        1.52 -     3.04: 661
        3.04 -     4.56: 41
        4.56 -     6.08: 10
        6.08 -     7.61: 2
  Bond angle restraints: 21978
  Sorted by residual:
  angle pdb=" N   ASN B   4 "
        pdb=" CA  ASN B   4 "
        pdb=" C   ASN B   4 "
      ideal   model   delta    sigma   weight residual
     111.75  106.25    5.50 1.28e+00 6.10e-01 1.85e+01
  angle pdb=" CA  TYR B 125 "
        pdb=" CB  TYR B 125 "
        pdb=" CG  TYR B 125 "
      ideal   model   delta    sigma   weight residual
     113.90  107.05    6.85 1.80e+00 3.09e-01 1.45e+01
  angle pdb=" CA  GLU B   5 "
        pdb=" C   GLU B   5 "
        pdb=" O   GLU B   5 "
      ideal   model   delta    sigma   weight residual
     120.80  116.93    3.87 1.05e+00 9.07e-01 1.36e+01
  angle pdb=" C   LEU B   6 "
        pdb=" N   VAL B   7 "
        pdb=" CA  VAL B   7 "
      ideal   model   delta    sigma   weight residual
     120.30  125.60   -5.30 1.64e+00 3.72e-01 1.04e+01
  angle pdb=" CA  LEU B   6 "
        pdb=" C   LEU B   6 "
        pdb=" O   LEU B   6 "
      ideal   model   delta    sigma   weight residual
     120.63  117.47    3.16 1.08e+00 8.57e-01 8.57e+00
  ... (remaining 21973 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.79: 5205
       17.79 -    35.59: 323
       35.59 -    53.38: 87
       53.38 -    71.18: 67
       71.18 -    88.97: 12
  Dihedral angle restraints: 5694
    sinusoidal: 3116
      harmonic: 2578
  Sorted by residual:
  dihedral pdb=" CA  THR C 205 "
           pdb=" C   THR C 205 "
           pdb=" N   LEU C 206 "
           pdb=" CA  LEU C 206 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.99  -29.01     0      5.00e+00 4.00e-02 3.37e+01
  dihedral pdb=" CA  GLN C 111 "
           pdb=" C   GLN C 111 "
           pdb=" N   ALA C 112 "
           pdb=" CA  ALA C 112 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.36   28.64     0      5.00e+00 4.00e-02 3.28e+01
  dihedral pdb=" CA  GLU A 703 "
           pdb=" C   GLU A 703 "
           pdb=" N   ARG A 704 "
           pdb=" CA  ARG A 704 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.85   28.15     0      5.00e+00 4.00e-02 3.17e+01
  ... (remaining 5691 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 609
       0.038 -    0.076: 242
       0.076 -    0.114: 43
       0.114 -    0.152: 15
       0.152 -    0.190: 3
  Chirality restraints: 912
  Sorted by residual:
  chirality pdb=" CA  LEU B   6 "
            pdb=" N   LEU B   6 "
            pdb=" C   LEU B   6 "
            pdb=" CB  LEU B   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 9.04e-01
  chirality pdb=" CA  GLN C 111 "
            pdb=" N   GLN C 111 "
            pdb=" C   GLN C 111 "
            pdb=" CB  GLN C 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.42e-01
  chirality pdb=" CA  TYR C 125 "
            pdb=" N   TYR C 125 "
            pdb=" C   TYR C 125 "
            pdb=" CB  TYR C 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.16e-01
  ... (remaining 909 not shown)

  Planarity restraints: 1770
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B   4 "   -0.199 2.00e-02 2.50e+03   4.13e-01 2.56e+03
        pdb=" CG  ASN B   4 "    0.018 2.00e-02 2.50e+03
        pdb=" OD1 ASN B   4 "    0.192 2.00e-02 2.50e+03
        pdb=" ND2 ASN B   4 "    0.002 2.00e-02 2.50e+03
        pdb="HD21 ASN B   4 "   -0.694 2.00e-02 2.50e+03
        pdb="HD22 ASN B   4 "    0.681 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C  56 "   -0.008 9.50e-02 1.11e+02   4.41e-02 4.36e+01
        pdb=" NE  ARG C  56 "    0.041 2.00e-02 2.50e+03
        pdb=" CZ  ARG C  56 "   -0.038 2.00e-02 2.50e+03
        pdb=" NH1 ARG C  56 "   -0.082 2.00e-02 2.50e+03
        pdb=" NH2 ARG C  56 "    0.017 2.00e-02 2.50e+03
        pdb="HH11 ARG C  56 "   -0.003 2.00e-02 2.50e+03
        pdb="HH12 ARG C  56 "    0.084 2.00e-02 2.50e+03
        pdb="HH21 ARG C  56 "   -0.000 2.00e-02 2.50e+03
        pdb="HH22 ARG C  56 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 127 "   -0.007 9.50e-02 1.11e+02   3.62e-02 2.95e+01
        pdb=" NE  ARG B 127 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 127 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 127 "   -0.054 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 127 "    0.053 2.00e-02 2.50e+03
        pdb="HH11 ARG B 127 "   -0.001 2.00e-02 2.50e+03
        pdb="HH12 ARG B 127 "    0.056 2.00e-02 2.50e+03
        pdb="HH21 ARG B 127 "    0.000 2.00e-02 2.50e+03
        pdb="HH22 ARG B 127 "   -0.053 2.00e-02 2.50e+03
  ... (remaining 1767 not shown)

  Histogram of nonbonded interaction distances:
        1.50 -     2.12: 376
        2.12 -     2.74: 22678
        2.74 -     3.36: 34851
        3.36 -     3.98: 42173
        3.98 -     4.60: 68345
  Nonbonded interactions: 168423
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 124 "
            pdb=" HH  TYR B 149 "
     model   vdw
     1.503 2.450
  nonbonded pdb=" O   GLU C 209 "
            pdb=" HG  SER C 210 "
     model   vdw
     1.503 2.450
  nonbonded pdb=" OE1 GLN A 653 "
            pdb=" HG  SER A 657 "
     model   vdw
     1.540 2.450
  nonbonded pdb=" O   SER B 210 "
            pdb=" HG  SER B 214 "
     model   vdw
     1.545 2.450
  nonbonded pdb=" OD1 ASP A 249 "
            pdb=" HZ3 LYS A 267 "
     model   vdw
     1.569 2.450
  ... (remaining 168418 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'B' and (resid 2 through 69 or resid 73 through 102 or (resid 103 and (na \ 
me N or name CA or name C or name O or name CB or name H or name HA )) or resid  \ 
104 through 154 or resid 162 through 229))
  selection = (chain 'C' and (resid 2 through 4 or (resid 5 and (name N or name CA or name C o \ 
r name O or name CB or name CG or name CD or name OE1 or name OE2 or name H or n \ 
ame HA )) or resid 6 through 133 or resid 138 through 229))
}

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 group one per residue
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:             0.990
  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:             0.200
  Extract box with map and model:          0.430
  Check model and map are aligned:         0.090
  Set scattering table:                    0.100
  Process input model:                     32.720
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7457
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   0.043   6141  Z= 0.259
  Angle     :  0.725   6.853   8251  Z= 0.437
  Chirality :  0.042   0.190    912
  Planarity :  0.006   0.055   1051
  Dihedral  : 13.899  88.973   2327
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 3.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  2.29 %
    Favored  : 97.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.00 (0.28), residues: 722
  helix: -1.21 (0.20), residues: 454
  sheet: -1.89 (0.95), residues: 27
  loop : -1.11 (0.41), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.006   TRP A 619 
 HIS   0.009   0.003   HIS A 725 
 PHE   0.015   0.002   PHE C 153 
 TYR   0.034   0.005   TYR B  48 
 ARG   0.023   0.003   ARG C  56 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.20350 (  383)
  hydrogen bonds       : angle       8.30202 ( 1134)
  metal coordination   : bond        0.00633 (    6)
  covalent geometry    : bond        0.00540 ( 6135)
  covalent geometry    : angle       0.72502 ( 8251)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  103 is missing expected H atoms. Skipping.
Evaluate side-chains
  190 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 188
  time to evaluate  : 0.876 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  545 GLU cc_start: 0.6825 (tt0) cc_final: 0.6532 (tm-30)
REVERT: A  716 LEU cc_start: 0.9304 (mt) cc_final: 0.8998 (mp)
REVERT: B  108 ASN cc_start: 0.8223 (m110) cc_final: 0.7865 (t0)
  outliers start: 2
  outliers final: 2
  residues processed: 189
  average time/residue: 0.5148
  time to fit residues: 119.8525
Evaluate side-chains
  114 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 112
  time to evaluate  : 1.005 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  581 ASN
Chi-restraints excluded: chain C residue  137 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 55 optimal weight:    0.0870
   chunk 30 optimal weight:    3.9990
   chunk 18 optimal weight:   20.0000
   chunk 37 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 34 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9990
   chunk 66 optimal weight:    3.9990
   overall best weight:    0.7562

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

Flipped N/Q/H residues before XYZ refinement:
A 262 GLN
A 461 GLN
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 664 GLN
B   4 ASN
B 144 GLN
B 224 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.129414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.099953 restraints weight = 44059.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.103369 restraints weight = 17826.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.105258 restraints weight = 10353.788|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.3450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6141  Z= 0.166
  Angle     :  0.682   5.224   8251  Z= 0.382
  Chirality :  0.037   0.169    912
  Planarity :  0.005   0.045   1051
  Dihedral  :  6.173  29.177    822
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 12.37 %
    Favored  : 85.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.76 (0.29), residues: 722
  helix:  0.05 (0.22), residues: 470
  sheet: -1.87 (0.68), residues: 42
  loop : -1.21 (0.43), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  59 
 HIS   0.008   0.001   HIS A 585 
 PHE   0.014   0.001   PHE A 707 
 TYR   0.024   0.002   TYR C 126 
 ARG   0.006   0.001   ARG A 558 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06182 (  383)
  hydrogen bonds       : angle       5.39555 ( 1134)
  metal coordination   : bond        0.00204 (    6)
  covalent geometry    : bond        0.00339 ( 6135)
  covalent geometry    : angle       0.68190 ( 8251)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  103 is missing expected H atoms. Skipping.
Evaluate side-chains
  148 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 136
  time to evaluate  : 0.881 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  545 GLU cc_start: 0.7013 (tt0) cc_final: 0.6631 (tm-30)
REVERT: A  689 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8699 (tpt)
REVERT: B  100 LEU cc_start: 0.8995 (mp) cc_final: 0.8765 (tp)
REVERT: B  108 ASN cc_start: 0.8078 (m110) cc_final: 0.7733 (t0)
REVERT: C   26 MET cc_start: 0.9023 (tpt) cc_final: 0.8622 (tpt)
REVERT: C  222 ARG cc_start: 0.8441 (mtp180) cc_final: 0.8199 (mtp180)
  outliers start: 12
  outliers final: 8
  residues processed: 140
  average time/residue: 0.4145
  time to fit residues: 75.0298
Evaluate side-chains
  112 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 103
  time to evaluate  : 1.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  517 MET
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  689 MET
Chi-restraints excluded: chain A residue  696 CYS
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   74 LYS
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain C residue   61 VAL
Chi-restraints excluded: chain C residue  102 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 7 optimal weight:    8.9990
   chunk 62 optimal weight:    0.4980
   chunk 69 optimal weight:    0.8980
   chunk 54 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 9 optimal weight:   10.0000
   chunk 17 optimal weight:    6.9990
   chunk 1 optimal weight:    3.9990
   overall best weight:    2.4786

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

Flipped N/Q/H residues before XYZ refinement:
A 461 GLN
C 219 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.126347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.096901 restraints weight = 45509.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.100233 restraints weight = 18964.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.102125 restraints weight = 11204.411|
|-----------------------------------------------------------------------------|
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.4119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   6141  Z= 0.215
  Angle     :  0.646   7.368   8251  Z= 0.366
  Chirality :  0.036   0.176    912
  Planarity :  0.004   0.044   1051
  Dihedral  :  5.776  25.925    818
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 14.50 %
    Favored  : 83.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.67 (0.29), residues: 722
  helix:  0.19 (0.22), residues: 472
  sheet: -1.50 (0.70), residues: 38
  loop : -1.46 (0.40), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  59 
 HIS   0.007   0.001   HIS B 164 
 PHE   0.012   0.001   PHE A 707 
 TYR   0.022   0.002   TYR B 125 
 ARG   0.003   0.000   ARG B 127 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05522 (  383)
  hydrogen bonds       : angle       5.21895 ( 1134)
  metal coordination   : bond        0.00409 (    6)
  covalent geometry    : bond        0.00445 ( 6135)
  covalent geometry    : angle       0.64634 ( 8251)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  103 is missing expected H atoms. Skipping.
Evaluate side-chains
  123 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 0.936 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  545 GLU cc_start: 0.6983 (tt0) cc_final: 0.6649 (tm-30)
REVERT: A  586 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7904 (tm-30)
REVERT: B  100 LEU cc_start: 0.9034 (mp) cc_final: 0.8825 (tp)
REVERT: C   26 MET cc_start: 0.8958 (tpt) cc_final: 0.8578 (tpt)
  outliers start: 16
  outliers final: 12
  residues processed: 115
  average time/residue: 0.4194
  time to fit residues: 64.7862
Evaluate side-chains
  112 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 1.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  364 SER
Chi-restraints excluded: chain A residue  368 ASN
Chi-restraints excluded: chain A residue  517 MET
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  696 CYS
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain B residue   74 LYS
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain C residue    6 LEU
Chi-restraints excluded: chain C residue   61 VAL
Chi-restraints excluded: chain C residue  102 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 18 optimal weight:   20.0000
   chunk 19 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 11 optimal weight:    9.9990
   chunk 45 optimal weight:    0.6980
   chunk 33 optimal weight:    6.9990
   chunk 42 optimal weight:    2.9990
   chunk 25 optimal weight:    7.9990
   chunk 29 optimal weight:    5.9990
   chunk 16 optimal weight:    7.9990
   chunk 70 optimal weight:    5.9990
   overall best weight:    3.3388

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

Flipped N/Q/H residues before XYZ refinement:
** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 461 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.125378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.095402 restraints weight = 45431.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.098725 restraints weight = 19495.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.100643 restraints weight = 11755.174|
|-----------------------------------------------------------------------------|
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.4439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   6141  Z= 0.258
  Angle     :  0.657   7.324   8251  Z= 0.372
  Chirality :  0.037   0.182    912
  Planarity :  0.004   0.049   1051
  Dihedral  :  5.574  23.539    818
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 15.88 %
    Favored  : 81.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.74 (0.29), residues: 722
  helix:  0.17 (0.23), residues: 474
  sheet: -2.21 (0.77), residues: 28
  loop : -1.54 (0.38), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 228 
 HIS   0.008   0.001   HIS B 164 
 PHE   0.011   0.001   PHE A 595 
 TYR   0.025   0.002   TYR B 125 
 ARG   0.003   0.000   ARG B 127 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05056 (  383)
  hydrogen bonds       : angle       5.18379 ( 1134)
  metal coordination   : bond        0.00704 (    6)
  covalent geometry    : bond        0.00531 ( 6135)
  covalent geometry    : angle       0.65686 ( 8251)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  103 is missing expected H atoms. Skipping.
Evaluate side-chains
  113 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 1.040 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  545 GLU cc_start: 0.7056 (tt0) cc_final: 0.6729 (tm-30)
REVERT: A  586 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7838 (tm-30)
REVERT: C   26 MET cc_start: 0.8973 (tpt) cc_final: 0.8568 (tpt)
  outliers start: 16
  outliers final: 12
  residues processed: 104
  average time/residue: 0.4045
  time to fit residues: 55.3651
Evaluate side-chains
  104 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 1.012 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  364 SER
Chi-restraints excluded: chain A residue  368 ASN
Chi-restraints excluded: chain A residue  517 MET
Chi-restraints excluded: chain A residue  696 CYS
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain B residue   74 LYS
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain C residue   61 VAL
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain C residue  116 VAL
Chi-restraints excluded: chain C residue  137 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 62 optimal weight:    0.0170
   chunk 8 optimal weight:   30.0000
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 66 optimal weight:    0.4980
   chunk 41 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 25 optimal weight:    8.9990
   chunk 18 optimal weight:    4.9990
   overall best weight:    0.9024

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

Flipped N/Q/H residues before XYZ refinement:
** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 461 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.128001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.097849 restraints weight = 44779.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.101285 restraints weight = 19036.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.103244 restraints weight = 11368.104|
|-----------------------------------------------------------------------------|
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.4741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6141  Z= 0.130
  Angle     :  0.571   5.362   8251  Z= 0.313
  Chirality :  0.034   0.145    912
  Planarity :  0.004   0.045   1051
  Dihedral  :  5.312  26.812    818
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 16.49 %
    Favored  : 81.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.30), residues: 722
  helix:  0.61 (0.23), residues: 474
  sheet: -1.88 (0.66), residues: 38
  loop : -1.33 (0.41), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  59 
 HIS   0.004   0.001   HIS A 585 
 PHE   0.011   0.001   PHE A 707 
 TYR   0.018   0.002   TYR A 640 
 ARG   0.002   0.000   ARG A 575 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04644 (  383)
  hydrogen bonds       : angle       4.63889 ( 1134)
  metal coordination   : bond        0.00172 (    6)
  covalent geometry    : bond        0.00284 ( 6135)
  covalent geometry    : angle       0.57097 ( 8251)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  103 is missing expected H atoms. Skipping.
Evaluate side-chains
  111 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 0.905 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  545 GLU cc_start: 0.7000 (tt0) cc_final: 0.6725 (tm-30)
REVERT: A  586 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7756 (tm-30)
REVERT: B  108 ASN cc_start: 0.8036 (m-40) cc_final: 0.7345 (t0)
REVERT: C   26 MET cc_start: 0.8956 (tpt) cc_final: 0.8586 (tpt)
  outliers start: 12
  outliers final: 10
  residues processed: 106
  average time/residue: 0.4013
  time to fit residues: 56.3079
Evaluate side-chains
  103 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 93
  time to evaluate  : 1.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  364 SER
Chi-restraints excluded: chain A residue  368 ASN
Chi-restraints excluded: chain A residue  517 MET
Chi-restraints excluded: chain A residue  696 CYS
Chi-restraints excluded: chain B residue   40 GLU
Chi-restraints excluded: chain B residue   74 LYS
Chi-restraints excluded: chain B residue  160 MET
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain C residue  116 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 25 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9990
   chunk 2 optimal weight:    4.9990
   chunk 10 optimal weight:    9.9990
   chunk 54 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   chunk 49 optimal weight:    6.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 461 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 = 0.3972 r_free = 0.3972 target = 0.125657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.095606 restraints weight = 45655.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.098963 restraints weight = 19548.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.100886 restraints weight = 11697.994|
|-----------------------------------------------------------------------------|
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.4871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   6141  Z= 0.217
  Angle     :  0.601   5.380   8251  Z= 0.338
  Chirality :  0.035   0.179    912
  Planarity :  0.004   0.043   1051
  Dihedral  :  5.211  21.971    818
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 17.25 %
    Favored  : 80.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.23 (0.30), residues: 722
  helix:  0.62 (0.23), residues: 466
  sheet: -2.24 (0.78), residues: 28
  loop : -1.36 (0.39), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 228 
 HIS   0.006   0.001   HIS B 164 
 PHE   0.009   0.001   PHE A 707 
 TYR   0.022   0.002   TYR B 125 
 ARG   0.003   0.000   ARG B 127 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04483 (  383)
  hydrogen bonds       : angle       4.80220 ( 1134)
  metal coordination   : bond        0.00526 (    6)
  covalent geometry    : bond        0.00452 ( 6135)
  covalent geometry    : angle       0.60088 ( 8251)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  103 is missing expected H atoms. Skipping.
Evaluate side-chains
  106 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.989 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  545 GLU cc_start: 0.7035 (tt0) cc_final: 0.6760 (tm-30)
REVERT: A  586 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7756 (tm-30)
REVERT: C   26 MET cc_start: 0.8960 (tpt) cc_final: 0.8575 (tpt)
  outliers start: 16
  outliers final: 15
  residues processed: 99
  average time/residue: 0.4135
  time to fit residues: 53.7204
Evaluate side-chains
  104 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 89
  time to evaluate  : 1.016 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  241 THR
Chi-restraints excluded: chain A residue  364 SER
Chi-restraints excluded: chain A residue  368 ASN
Chi-restraints excluded: chain A residue  517 MET
Chi-restraints excluded: chain A residue  696 CYS
Chi-restraints excluded: chain B residue   40 GLU
Chi-restraints excluded: chain B residue   45 SER
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain B residue   74 LYS
Chi-restraints excluded: chain B residue   78 MET
Chi-restraints excluded: chain B residue   94 CYS
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain C residue   61 VAL
Chi-restraints excluded: chain C residue  106 ILE
Chi-restraints excluded: chain C residue  137 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 9 optimal weight:    8.9990
   chunk 13 optimal weight:   10.0000
   chunk 19 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9980
   chunk 6 optimal weight:   20.0000
   chunk 29 optimal weight:    4.9990
   chunk 59 optimal weight:    1.9990
   chunk 54 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
** A 257 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 = 0.3991 r_free = 0.3991 target = 0.126874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.096835 restraints weight = 44788.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.100222 restraints weight = 19048.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.102018 restraints weight = 11365.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.5090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6141  Z= 0.146
  Angle     :  0.560   5.643   8251  Z= 0.308
  Chirality :  0.035   0.177    912
  Planarity :  0.004   0.040   1051
  Dihedral  :  5.087  25.227    818
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 18.32 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.30), residues: 722
  helix:  0.87 (0.23), residues: 468
  sheet: -2.23 (0.78), residues: 28
  loop : -1.30 (0.40), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  59 
 HIS   0.004   0.001   HIS A 585 
 PHE   0.009   0.001   PHE A 707 
 TYR   0.014   0.002   TYR B 125 
 ARG   0.003   0.000   ARG A 626 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04262 (  383)
  hydrogen bonds       : angle       4.55176 ( 1134)
  metal coordination   : bond        0.00308 (    6)
  covalent geometry    : bond        0.00309 ( 6135)
  covalent geometry    : angle       0.55982 ( 8251)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  103 is missing expected H atoms. Skipping.
Evaluate side-chains
  105 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 0.980 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  545 GLU cc_start: 0.7012 (tt0) cc_final: 0.6716 (tm-30)
REVERT: A  586 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7730 (tm-30)
REVERT: C   26 MET cc_start: 0.8953 (tpt) cc_final: 0.8571 (tpt)
  outliers start: 11
  outliers final: 9
  residues processed: 100
  average time/residue: 0.4014
  time to fit residues: 53.2651
Evaluate side-chains
  101 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 0.933 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  364 SER
Chi-restraints excluded: chain A residue  368 ASN
Chi-restraints excluded: chain A residue  678 LEU
Chi-restraints excluded: chain A residue  696 CYS
Chi-restraints excluded: chain B residue   40 GLU
Chi-restraints excluded: chain B residue   74 LYS
Chi-restraints excluded: chain B residue   78 MET
Chi-restraints excluded: chain B residue   94 CYS
Chi-restraints excluded: chain B residue  206 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 6 optimal weight:   20.0000
   chunk 54 optimal weight:    4.9990
   chunk 50 optimal weight:    4.9990
   chunk 27 optimal weight:    4.9990
   chunk 42 optimal weight:    3.9990
   chunk 30 optimal weight:    4.9990
   chunk 21 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9980
   chunk 52 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 512 ASN
B  95 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.126873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.096778 restraints weight = 45095.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.100009 restraints weight = 19407.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.101878 restraints weight = 11545.317|
|-----------------------------------------------------------------------------|
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.5226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6141  Z= 0.152
  Angle     :  0.558   5.503   8251  Z= 0.308
  Chirality :  0.035   0.145    912
  Planarity :  0.004   0.039   1051
  Dihedral  :  4.979  24.013    818
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 18.02 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.31), residues: 722
  helix:  1.01 (0.23), residues: 468
  sheet: -2.19 (0.79), residues: 28
  loop : -1.23 (0.41), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  59 
 HIS   0.006   0.001   HIS B 164 
 PHE   0.008   0.001   PHE A 707 
 TYR   0.016   0.002   TYR B 125 
 ARG   0.002   0.000   ARG B 127 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04140 (  383)
  hydrogen bonds       : angle       4.49493 ( 1134)
  metal coordination   : bond        0.00310 (    6)
  covalent geometry    : bond        0.00320 ( 6135)
  covalent geometry    : angle       0.55803 ( 8251)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  103 is missing expected H atoms. Skipping.
Evaluate side-chains
  104 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 0.931 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  545 GLU cc_start: 0.7037 (tt0) cc_final: 0.6726 (tm-30)
REVERT: A  586 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7703 (tm-30)
REVERT: C   26 MET cc_start: 0.8941 (tpt) cc_final: 0.8551 (tpt)
  outliers start: 13
  outliers final: 12
  residues processed: 97
  average time/residue: 0.4058
  time to fit residues: 51.6877
Evaluate side-chains
  101 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  364 SER
Chi-restraints excluded: chain A residue  368 ASN
Chi-restraints excluded: chain A residue  517 MET
Chi-restraints excluded: chain A residue  678 LEU
Chi-restraints excluded: chain A residue  696 CYS
Chi-restraints excluded: chain A residue  702 ASP
Chi-restraints excluded: chain B residue   40 GLU
Chi-restraints excluded: chain B residue   45 SER
Chi-restraints excluded: chain B residue   78 MET
Chi-restraints excluded: chain B residue   94 CYS
Chi-restraints excluded: chain B residue  206 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 33 optimal weight:    4.9990
   chunk 47 optimal weight:    2.9990
   chunk 1 optimal weight:    5.9990
   chunk 29 optimal weight:    5.9990
   chunk 17 optimal weight:   10.0000
   chunk 46 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9980
   chunk 66 optimal weight:    2.9990
   chunk 5 optimal weight:    7.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 461 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.128102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.098083 restraints weight = 45015.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.101269 restraints weight = 19370.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.103173 restraints weight = 11564.374|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.5395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6141  Z= 0.134
  Angle     :  0.548   5.527   8251  Z= 0.298
  Chirality :  0.034   0.137    912
  Planarity :  0.003   0.042   1051
  Dihedral  :  4.850  24.328    818
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 18.17 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.31), residues: 722
  helix:  1.21 (0.24), residues: 467
  sheet: -2.24 (0.80), residues: 28
  loop : -1.20 (0.41), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  59 
 HIS   0.004   0.001   HIS A 585 
 PHE   0.008   0.001   PHE A 707 
 TYR   0.013   0.002   TYR B 125 
 ARG   0.002   0.000   ARG B 127 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03994 (  383)
  hydrogen bonds       : angle       4.37312 ( 1134)
  metal coordination   : bond        0.00268 (    6)
  covalent geometry    : bond        0.00285 ( 6135)
  covalent geometry    : angle       0.54788 ( 8251)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  103 is missing expected H atoms. Skipping.
Evaluate side-chains
  105 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.890 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  545 GLU cc_start: 0.6937 (tt0) cc_final: 0.6700 (tm-30)
REVERT: A  586 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7674 (tm-30)
REVERT: A  687 LYS cc_start: 0.7595 (pttt) cc_final: 0.7269 (pttt)
REVERT: C   26 MET cc_start: 0.8868 (tpt) cc_final: 0.8511 (tpt)
  outliers start: 12
  outliers final: 10
  residues processed: 100
  average time/residue: 0.3714
  time to fit residues: 49.6148
Evaluate side-chains
  98 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  364 SER
Chi-restraints excluded: chain A residue  368 ASN
Chi-restraints excluded: chain A residue  517 MET
Chi-restraints excluded: chain A residue  678 LEU
Chi-restraints excluded: chain A residue  702 ASP
Chi-restraints excluded: chain B residue   40 GLU
Chi-restraints excluded: chain B residue   45 SER
Chi-restraints excluded: chain B residue   78 MET
Chi-restraints excluded: chain B residue   94 CYS
Chi-restraints excluded: chain B residue  206 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 16 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9980
   chunk 43 optimal weight:    3.9990
   chunk 4 optimal weight:    6.9990
   chunk 18 optimal weight:   20.0000
   chunk 51 optimal weight:    3.9990
   chunk 45 optimal weight:    0.2980
   chunk 64 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 44 optimal weight:    0.5980
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 461 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 = 0.4001 r_free = 0.4001 target = 0.127183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.097191 restraints weight = 44752.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.100477 restraints weight = 19363.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.102375 restraints weight = 11479.681|
|-----------------------------------------------------------------------------|
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.5490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6141  Z= 0.139
  Angle     :  0.551   5.439   8251  Z= 0.302
  Chirality :  0.035   0.191    912
  Planarity :  0.004   0.042   1051
  Dihedral  :  4.769  23.854    818
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 18.93 %
    Favored  : 79.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.31), residues: 722
  helix:  1.31 (0.24), residues: 466
  sheet: -2.23 (0.81), residues: 28
  loop : -1.18 (0.41), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  59 
 HIS   0.004   0.001   HIS B 164 
 PHE   0.008   0.001   PHE A 707 
 TYR   0.015   0.002   TYR A 640 
 ARG   0.002   0.000   ARG B 127 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03988 (  383)
  hydrogen bonds       : angle       4.34681 ( 1134)
  metal coordination   : bond        0.00268 (    6)
  covalent geometry    : bond        0.00295 ( 6135)
  covalent geometry    : angle       0.55122 ( 8251)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  103 is missing expected H atoms. Skipping.
Evaluate side-chains
  97 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 87
  time to evaluate  : 1.018 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  545 GLU cc_start: 0.6927 (tt0) cc_final: 0.6689 (tm-30)
REVERT: A  570 LYS cc_start: 0.8593 (mmmt) cc_final: 0.8037 (mttt)
REVERT: A  586 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7700 (tm-30)
REVERT: A  640 TYR cc_start: 0.8361 (t80) cc_final: 0.8126 (t80)
REVERT: A  687 LYS cc_start: 0.7585 (pttt) cc_final: 0.7260 (pttt)
REVERT: C   26 MET cc_start: 0.8921 (tpt) cc_final: 0.8536 (tpt)
  outliers start: 10
  outliers final: 10
  residues processed: 93
  average time/residue: 0.3951
  time to fit residues: 48.8884
Evaluate side-chains
  96 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 1.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  364 SER
Chi-restraints excluded: chain A residue  368 ASN
Chi-restraints excluded: chain A residue  678 LEU
Chi-restraints excluded: chain A residue  702 ASP
Chi-restraints excluded: chain B residue   40 GLU
Chi-restraints excluded: chain B residue   45 SER
Chi-restraints excluded: chain B residue   78 MET
Chi-restraints excluded: chain B residue   94 CYS
Chi-restraints excluded: chain B residue  206 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 61 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   chunk 72 optimal weight:    3.9990
   chunk 60 optimal weight:    0.8980
   chunk 9 optimal weight:    4.9990
   chunk 42 optimal weight:    3.9990
   chunk 12 optimal weight:   10.0000
   chunk 17 optimal weight:    0.7980
   chunk 49 optimal weight:    6.9990
   overall best weight:    1.9184

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

Flipped N/Q/H residues before XYZ refinement:
** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 461 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 = 0.3993 r_free = 0.3993 target = 0.126802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.096707 restraints weight = 45257.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.099905 restraints weight = 19508.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.101805 restraints weight = 11640.057|
|-----------------------------------------------------------------------------|
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.5550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6141  Z= 0.164
  Angle     :  0.557   5.433   8251  Z= 0.307
  Chirality :  0.034   0.141    912
  Planarity :  0.004   0.042   1051
  Dihedral  :  4.728  22.776    818
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 19.24 %
    Favored  : 79.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.31), residues: 722
  helix:  1.24 (0.24), residues: 467
  sheet: -2.30 (0.82), residues: 28
  loop : -1.23 (0.41), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B  59 
 HIS   0.006   0.001   HIS B 164 
 PHE   0.008   0.001   PHE A 707 
 TYR   0.018   0.002   TYR B 125 
 ARG   0.002   0.000   ARG B 127 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03951 (  383)
  hydrogen bonds       : angle       4.38735 ( 1134)
  metal coordination   : bond        0.00391 (    6)
  covalent geometry    : bond        0.00345 ( 6135)
  covalent geometry    : angle       0.55656 ( 8251)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4299.69 seconds
wall clock time: 74 minutes 14.44 seconds (4454.44 seconds total)