Starting phenix.real_space_refine
on Wed Sep 17 17:49:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yjv_39351/09_2025/8yjv_39351.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yjv_39351/09_2025/8yjv_39351.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.51
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yjv_39351/09_2025/8yjv_39351.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yjv_39351/09_2025/8yjv_39351.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yjv_39351/09_2025/8yjv_39351.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yjv_39351/09_2025/8yjv_39351.cif"
  }
  resolution = 3.51
  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=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 404 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      64      5.49       5
     S      61      5.16       5
     C    6057      2.51       5
     N    1667      2.21       5
     O    2089      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9938
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "C"
      Number of atoms: 1947
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 253, 1947
          Classifications: {'peptide': 253}
          Link IDs: {'PTRANS': 7, 'TRANS': 245}
    Chain: "D"
      Number of atoms: 2779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 353, 2779
          Classifications: {'peptide': 353}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 15, 'TRANS': 337}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "A"
      Number of atoms: 1946
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 253, 1946
          Classifications: {'peptide': 253}
          Link IDs: {'PTRANS': 7, 'TRANS': 245}
    Chain: "B"
      Number of atoms: 1938
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 252, 1938
          Classifications: {'peptide': 252}
          Link IDs: {'PTRANS': 7, 'TRANS': 244}
    Chain: "J"
      Number of atoms: 406
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 406
          Classifications: {'DNA': 20}
          Link IDs: {'rna3p': 19}
    Chain: "E"
      Number of atoms: 635
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 635
          Classifications: {'DNA': 31}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 30}
    Chain: "F"
      Number of atoms: 227
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 227
          Classifications: {'DNA': 11}
          Link IDs: {'rna3p': 10}
    Chain: "H"
      Number of atoms: 60
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 60
          Classifications: {'DNA': 3}
          Link IDs: {'rna3p': 2}
  Time building chain proxies: 2.41, per 1000 atoms: 0.24
  Number of scatterers: 9938
  At special positions: 0
  Unit cell: (108.73, 107.07, 105.41, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      61     16.00
     P      64     15.00
     O    2089      8.00
     N    1667      7.00
     C    6057      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 135 " - pdb=" SG  CYS A 162 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 135 " - pdb=" SG  CYS B 162 " distance=2.03

  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: 0.81
  Conformation dependent library (CDL) restraints added in 265.6 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2098

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 14 sheets defined
      31.9% alpha, 24.2% beta
      12 base pairs and 48 stacking pairs defined.
    Time for finding SS restraints: 0.99
  Creating SS restraints...
    Processing helix  chain 'C' and resid 8 through 19
      removed outlier: 4.243A  pdb=" N   LEU C  12 " --> pdb=" O   GLN C   8 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 72 through 80
    Processing helix  chain 'C' and resid 141 through 155
      removed outlier: 4.132A  pdb=" N   HIS C 153 " --> pdb=" O   ARG C 149 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   ILE C 154 " --> pdb=" O   ASP C 150 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 209 through 216
    Processing helix  chain 'C' and resid 217 through 222
      Proline residue:  C 220  - end of helix
      No H-bonds generated for 'chain 'C' and resid 217 through 222'
    Processing helix  chain 'D' and resid 6 through 13
    Processing helix  chain 'D' and resid 23 through 27
      removed outlier: 3.796A  pdb=" N   TYR D  26 " --> pdb=" O   ILE D  23 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   PHE D  27 " --> pdb=" O   LYS D  24 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 23 through 27'
    Processing helix  chain 'D' and resid 35 through 46
    Processing helix  chain 'D' and resid 61 through 77
      removed outlier: 3.536A  pdb=" N   ASN D  77 " --> pdb=" O   ARG D  73 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 92
      No H-bonds generated for 'chain 'D' and resid 90 through 92'
    Processing helix  chain 'D' and resid 93 through 118
    Processing helix  chain 'D' and resid 120 through 129
    Processing helix  chain 'D' and resid 134 through 149
    Processing helix  chain 'D' and resid 158 through 169
      removed outlier: 3.698A  pdb=" N   SER D 162 " --> pdb=" O   GLU D 158 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 180 through 186
      removed outlier: 3.894A  pdb=" N   THR D 184 " --> pdb=" O   MET D 180 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 209 through 216
    Processing helix  chain 'D' and resid 219 through 231
    Processing helix  chain 'D' and resid 242 through 254
    Processing helix  chain 'D' and resid 256 through 262
    Processing helix  chain 'D' and resid 275 through 285
    Processing helix  chain 'D' and resid 302 through 313
    Processing helix  chain 'D' and resid 317 through 334
      removed outlier: 3.802A  pdb=" N   ILE D 321 " --> pdb=" O   SER D 317 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 335 through 337
      No H-bonds generated for 'chain 'D' and resid 335 through 337'
    Processing helix  chain 'D' and resid 339 through 343
    Processing helix  chain 'A' and resid 8 through 19
      removed outlier: 3.818A  pdb=" N   LEU A  12 " --> pdb=" O   GLN A   8 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 81
    Processing helix  chain 'A' and resid 141 through 152
    Processing helix  chain 'A' and resid 209 through 216
    Processing helix  chain 'A' and resid 217 through 222
      Proline residue:  A 220  - end of helix
      No H-bonds generated for 'chain 'A' and resid 217 through 222'
    Processing helix  chain 'B' and resid 8 through 20
      removed outlier: 4.096A  pdb=" N   LEU B  12 " --> pdb=" O   GLN B   8 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 72 through 82
      removed outlier: 3.682A  pdb=" N   ALA B  82 " --> pdb=" O   ILE B  78 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 152
    Processing helix  chain 'B' and resid 210 through 216
    Processing helix  chain 'B' and resid 217 through 222
      Proline residue:  B 220  - end of helix
      No H-bonds generated for 'chain 'B' and resid 217 through 222'
    Processing sheet with id=AA1, first strand: chain 'C' and resid 58 through 61
      removed outlier: 4.924A  pdb=" N   THR C  59 " --> pdb=" O   ARG C   5 " (cutoff:3.500A)
      removed outlier: 4.529A  pdb=" N   ARG C   5 " --> pdb=" O   THR C  59 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   SER B 172 " --> pdb=" O   ALA B 157 " (cutoff:3.500A)
      removed outlier: 6.244A  pdb=" N   ALA B 157 " --> pdb=" O   SER B 172 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 25 through 30
      removed outlier: 3.779A  pdb=" N   MET C  68 " --> pdb=" O   TRP C  28 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 34 through 40
      removed outlier: 5.527A  pdb=" N   SER C 230 " --> pdb=" O   PRO C 234 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   LYS C 240 " --> pdb=" O   THR C 224 " (cutoff:3.500A)
      removed outlier: 5.878A  pdb=" N   THR C 224 " --> pdb=" O   LYS C 240 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 126 through 127
      removed outlier: 4.027A  pdb=" N   LYS D 345 " --> pdb=" O   GLY C 127 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 204 through 208
    Processing sheet with id=AA6, first strand: chain 'D' and resid 18 through 21
    Processing sheet with id=AA7, first strand: chain 'D' and resid 152 through 154
      removed outlier: 3.755A  pdb=" N   ALA D 174 " --> pdb=" O   LYS D  30 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 47 through 48
    Processing sheet with id=AA9, first strand: chain 'A' and resid 59 through 61
    Processing sheet with id=AB1, first strand: chain 'A' and resid 66 through 71
      removed outlier: 7.288A  pdb=" N   GLU A  25 " --> pdb=" O   MET A  40 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   MET A  40 " --> pdb=" O   GLU A  25 " (cutoff:3.500A)
      removed outlier: 5.391A  pdb=" N   CYS A  27 " --> pdb=" O   GLN A  38 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   GLN A  38 " --> pdb=" O   CYS A  27 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LEU A 251 " --> pdb=" O   LEU A 235 " (cutoff:3.500A)
      removed outlier: 4.900A  pdb=" N   LYS A 240 " --> pdb=" O   THR A 224 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   THR A 224 " --> pdb=" O   LYS A 240 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 204 through 208
      removed outlier: 3.735A  pdb=" N   LEU A 205 " --> pdb=" O   ILE A 160 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   ILE A 160 " --> pdb=" O   LEU A 205 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 59 through 61
      removed outlier: 3.904A  pdb=" N   THR B  59 " --> pdb=" O   ARG B   5 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 25 through 30
    Processing sheet with id=AB5, first strand: chain 'B' and resid 34 through 40
      removed outlier: 3.728A  pdb=" N   LEU B 251 " --> pdb=" O   LEU B 235 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LEU B 235 " --> pdb=" O   LEU B 251 " (cutoff:3.500A)

    425 hydrogen bonds defined for protein.
    1182 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      24 hydrogen bonds
      48 hydrogen bond angles
      0 basepair planarities
      12 basepair parallelities
      48 stacking parallelities
  Total time for adding SS restraints: 1.65

  Time building geometry restraints manager: 1.08 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: 2315
        1.33 -     1.45: 2144
        1.45 -     1.57: 5536
        1.57 -     1.69: 127
        1.69 -     1.81: 98
  Bond restraints: 10220
  Sorted by residual:
  bond pdb=" N   THR C 219 "
       pdb=" CA  THR C 219 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.031 1.04e-02 9.25e+03 8.80e+00
  bond pdb=" C3'  DT E   3 "
       pdb=" O3'  DT E   3 "
    ideal  model  delta    sigma   weight residual
    1.422  1.496 -0.074 3.00e-02 1.11e+03 6.12e+00
  bond pdb=" N   THR C 216 "
       pdb=" CA  THR C 216 "
    ideal  model  delta    sigma   weight residual
    1.456  1.490 -0.034 1.44e-02 4.82e+03 5.57e+00
  bond pdb=" N   LEU C 221 "
       pdb=" CA  LEU C 221 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 1.30e-02 5.92e+03 5.30e+00
  bond pdb=" N   THR C 224 "
       pdb=" CA  THR C 224 "
    ideal  model  delta    sigma   weight residual
    1.457  1.485 -0.028 1.23e-02 6.61e+03 5.21e+00
  ... (remaining 10215 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.19: 13775
        3.19 -     6.38: 245
        6.38 -     9.58: 39
        9.58 -    12.77: 7
       12.77 -    15.96: 2
  Bond angle restraints: 14068
  Sorted by residual:
  angle pdb=" C   ALA C 242 "
        pdb=" N   ASP C 243 "
        pdb=" CA  ASP C 243 "
      ideal   model   delta    sigma   weight residual
     121.54  135.01  -13.47 1.91e+00 2.74e-01 4.97e+01
  angle pdb=" CA  PRO B 106 "
        pdb=" N   PRO B 106 "
        pdb=" CD  PRO B 106 "
      ideal   model   delta    sigma   weight residual
     112.00  104.02    7.98 1.40e+00 5.10e-01 3.25e+01
  angle pdb=" C   ALA B 242 "
        pdb=" N   ASP B 243 "
        pdb=" CA  ASP B 243 "
      ideal   model   delta    sigma   weight residual
     122.46  129.62   -7.16 1.41e+00 5.03e-01 2.58e+01
  angle pdb=" CA  LEU D 275 "
        pdb=" CB  LEU D 275 "
        pdb=" CG  LEU D 275 "
      ideal   model   delta    sigma   weight residual
     116.30  132.26  -15.96 3.50e+00 8.16e-02 2.08e+01
  angle pdb=" N   LYS C 217 "
        pdb=" CA  LYS C 217 "
        pdb=" C   LYS C 217 "
      ideal   model   delta    sigma   weight residual
     113.28  107.73    5.55 1.22e+00 6.72e-01 2.07e+01
  ... (remaining 14063 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.35: 5746
       35.35 -    70.69: 402
       70.69 -   106.04: 17
      106.04 -   141.39: 1
      141.39 -   176.73: 1
  Dihedral angle restraints: 6167
    sinusoidal: 2933
      harmonic: 3234
  Sorted by residual:
  dihedral pdb=" CB  CYS A 135 "
           pdb=" SG  CYS A 135 "
           pdb=" SG  CYS A 162 "
           pdb=" CB  CYS A 162 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  153.33  -60.33     1      1.00e+01 1.00e-02 4.85e+01
  dihedral pdb=" CA  ASP A 150 "
           pdb=" C   ASP A 150 "
           pdb=" N   LEU A 151 "
           pdb=" CA  LEU A 151 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.81   22.19     0      5.00e+00 4.00e-02 1.97e+01
  dihedral pdb=" CA  ILE B 241 "
           pdb=" C   ILE B 241 "
           pdb=" N   ALA B 242 "
           pdb=" CA  ALA B 242 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.21   19.79     0      5.00e+00 4.00e-02 1.57e+01
  ... (remaining 6164 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 1317
       0.073 -    0.145: 255
       0.145 -    0.218: 38
       0.218 -    0.290: 6
       0.290 -    0.363: 3
  Chirality restraints: 1619
  Sorted by residual:
  chirality pdb=" CB  VAL A 233 "
            pdb=" CA  VAL A 233 "
            pdb=" CG1 VAL A 233 "
            pdb=" CG2 VAL A 233 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.27   -0.36 2.00e-01 2.50e+01 3.29e+00
  chirality pdb=" CG  LEU B  72 "
            pdb=" CB  LEU B  72 "
            pdb=" CD1 LEU B  72 "
            pdb=" CD2 LEU B  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.29   -0.30 2.00e-01 2.50e+01 2.28e+00
  chirality pdb=" CG  LEU B 235 "
            pdb=" CB  LEU B 235 "
            pdb=" CD1 LEU B 235 "
            pdb=" CD2 LEU B 235 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.29   -0.30 2.00e-01 2.50e+01 2.20e+00
  ... (remaining 1616 not shown)

  Planarity restraints: 1591
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 233 "    0.068 5.00e-02 4.00e+02   1.03e-01 1.71e+01
        pdb=" N   PRO A 234 "   -0.179 5.00e-02 4.00e+02
        pdb=" CA  PRO A 234 "    0.055 5.00e-02 4.00e+02
        pdb=" CD  PRO A 234 "    0.055 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 214 "   -0.019 2.00e-02 2.50e+03   2.60e-02 1.18e+01
        pdb=" CG  PHE B 214 "    0.059 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 214 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 214 "   -0.023 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 214 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 214 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 214 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 214 "    0.018 2.00e-02 2.50e+03   2.50e-02 1.09e+01
        pdb=" CG  PHE C 214 "   -0.056 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 214 "    0.025 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 214 "    0.014 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 214 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 214 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 214 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1588 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.83: 2804
        2.83 -     3.35: 8286
        3.35 -     3.87: 17788
        3.87 -     4.38: 19625
        4.38 -     4.90: 33050
  Nonbonded interactions: 81553
  Sorted by model distance:
  nonbonded pdb=" O   MET D  67 "
            pdb=" OG1 THR D  71 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" O   THR B 216 "
            pdb=" OG1 THR B 219 "
     model   vdw
     2.338 3.040
  nonbonded pdb=" OG  SER D 197 "
            pdb=" OP2  DA E  14 "
     model   vdw
     2.342 3.040
  nonbonded pdb=" O   ASN B  71 "
            pdb=" OG  SER B  74 "
     model   vdw
     2.355 3.040
  nonbonded pdb=" N   GLY D   2 "
            pdb=" OD1 ASP D 179 "
     model   vdw
     2.383 3.120
  ... (remaining 81548 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 2 through 253)
  selection = chain 'B'
  selection = (chain 'C' and resid 2 through 253)
}

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:             3.310
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.200
  Find NCS groups from input model:        0.080
  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:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7271
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      :  0.007   0.099  10222  Z= 0.305
  Angle     :  1.084  15.960  14072  Z= 0.567
  Chirality :  0.060   0.363   1619
  Planarity :  0.008   0.103   1591
  Dihedral  : 20.737 176.732   4063
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.73 %
    Favored  : 99.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.60 (0.21), residues: 1103
  helix: -2.47 (0.22), residues: 308
  sheet: -2.02 (0.26), residues: 335
  loop : -2.42 (0.22), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG B   5 
 TYR   0.030   0.003   TYR A 249 
 PHE   0.059   0.005   PHE B 214 
 TRP   0.051   0.005   TRP D 274 
 HIS   0.016   0.002   HIS D 143 

Details of bonding type rmsd
  covalent geometry    : bond        0.00707 (10220)
  covalent geometry    : angle       1.08369 (14068)
  SS BOND              : bond        0.00067 (    2)
  SS BOND              : angle       1.35529 (    4)
  hydrogen bonds       : bond        0.20225 (  449)
  hydrogen bonds       : angle      10.17809 ( 1230)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 157
  time to evaluate  : 0.367 
Fit side-chains
REVERT: C   53 ARG cc_start: 0.7826 (mtm180) cc_final: 0.7393 (mtm180)
REVERT: C   97 ASP cc_start: 0.4939 (p0) cc_final: 0.4469 (p0)
REVERT: C  244 MET cc_start: 0.8524 (mtp) cc_final: 0.8227 (mtp)
REVERT: D   21 ASN cc_start: 0.7825 (m110) cc_final: 0.7594 (m110)
REVERT: A  199 MET cc_start: 0.5303 (ttm) cc_final: 0.4907 (ttm)
  outliers start: 1
  outliers final: 0
  residues processed: 158
  average time/residue: 0.0980
  time to fit residues: 22.3601
Evaluate side-chains
  118 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 108 optimal weight:    0.5980
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    0.4980
   chunk 113 optimal weight:    3.9990
   chunk 53 optimal weight:    0.0970
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0470
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.0770
   chunk 100 optimal weight:    0.9980
   overall best weight:    0.2634

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

Flipped N/Q/H residues before XYZ refinement:
D 137 HIS
** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 131 GLN
B 153 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.160644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.123523 restraints weight = 13077.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.127246 restraints weight = 7642.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.129758 restraints weight = 5357.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.131413 restraints weight = 4230.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.132565 restraints weight = 3603.947|
|-----------------------------------------------------------------------------|
r_work (final): 0.3661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7201
moved from start:          0.1431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063  10222  Z= 0.141
  Angle     :  0.601   7.331  14072  Z= 0.337
  Chirality :  0.043   0.151   1619
  Planarity :  0.005   0.080   1591
  Dihedral  : 21.577 167.963   1939
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  7.68 %
    Favored  : 91.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.52 (0.23), residues: 1103
  helix: -0.57 (0.27), residues: 314
  sheet: -1.95 (0.26), residues: 336
  loop : -2.10 (0.24), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B   5 
 TYR   0.010   0.001   TYR A 114 
 PHE   0.030   0.002   PHE B 214 
 TRP   0.018   0.002   TRP D 274 
 HIS   0.007   0.001   HIS D 143 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (10220)
  covalent geometry    : angle       0.60056 (14068)
  SS BOND              : bond        0.01239 (    2)
  SS BOND              : angle       0.99765 (    4)
  hydrogen bonds       : bond        0.05250 (  449)
  hydrogen bonds       : angle       6.96717 ( 1230)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 143
  time to evaluate  : 0.354 
Fit side-chains
REVERT: C   97 ASP cc_start: 0.4998 (p0) cc_final: 0.4303 (p0)
REVERT: C  214 PHE cc_start: 0.8630 (m-10) cc_final: 0.8360 (m-10)
REVERT: C  225 VAL cc_start: 0.8452 (t) cc_final: 0.8213 (p)
REVERT: D   77 ASN cc_start: 0.7942 (m-40) cc_final: 0.7459 (m110)
REVERT: D   92 LEU cc_start: 0.7828 (mp) cc_final: 0.7624 (mp)
REVERT: D  180 MET cc_start: 0.6922 (OUTLIER) cc_final: 0.5865 (mmt)
REVERT: B  131 GLN cc_start: 0.6556 (OUTLIER) cc_final: 0.6020 (mm-40)
  outliers start: 10
  outliers final: 7
  residues processed: 147
  average time/residue: 0.1003
  time to fit residues: 20.8579
Evaluate side-chains
  133 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 124
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  236 VAL
Chi-restraints excluded: chain D residue  180 MET
Chi-restraints excluded: chain D residue  321 ILE
Chi-restraints excluded: chain A residue   32 SER
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain B residue   24 ASN
Chi-restraints excluded: chain B residue  131 GLN
Chi-restraints excluded: chain B residue  206 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 71 optimal weight:    0.2980
   chunk 52 optimal weight:    0.6980
   chunk 60 optimal weight:    3.9990
   chunk 81 optimal weight:    1.9990
   chunk 114 optimal weight:    4.9990
   chunk 23 optimal weight:    0.3980
   chunk 5 optimal weight:    1.9990
   chunk 79 optimal weight:    3.9990
   chunk 67 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
C  36 ASN
** C  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 110 GLN
D 137 HIS
** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.156459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.118914 restraints weight = 13213.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.122608 restraints weight = 7735.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.125030 restraints weight = 5449.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.126684 restraints weight = 4336.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.127701 restraints weight = 3721.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.3601
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7317
moved from start:          0.1925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  10222  Z= 0.188
  Angle     :  0.612   7.904  14072  Z= 0.336
  Chirality :  0.043   0.150   1619
  Planarity :  0.004   0.074   1591
  Dihedral  : 21.453 167.971   1939
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 11.01 %
    Favored  : 87.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.14 (0.24), residues: 1103
  helix:  0.22 (0.29), residues: 315
  sheet: -1.94 (0.26), residues: 329
  loop : -2.09 (0.24), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  70 
 TYR   0.014   0.002   TYR D  83 
 PHE   0.029   0.002   PHE B 214 
 TRP   0.008   0.002   TRP D 274 
 HIS   0.005   0.001   HIS D 143 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 (10220)
  covalent geometry    : angle       0.61168 (14068)
  SS BOND              : bond        0.00219 (    2)
  SS BOND              : angle       0.87897 (    4)
  hydrogen bonds       : bond        0.04568 (  449)
  hydrogen bonds       : angle       6.56502 ( 1230)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 128
  time to evaluate  : 0.388 
Fit side-chains
REVERT: C   36 ASN cc_start: 0.8389 (OUTLIER) cc_final: 0.7770 (m-40)
REVERT: C   53 ARG cc_start: 0.8041 (mtm180) cc_final: 0.7535 (mtm180)
REVERT: C   97 ASP cc_start: 0.5019 (p0) cc_final: 0.4111 (p0)
REVERT: C  225 VAL cc_start: 0.8463 (t) cc_final: 0.8256 (p)
REVERT: B  146 ARG cc_start: 0.7072 (ttt90) cc_final: 0.6806 (ttt90)
  outliers start: 18
  outliers final: 12
  residues processed: 139
  average time/residue: 0.0901
  time to fit residues: 18.2410
Evaluate side-chains
  132 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 119
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   36 ASN
Chi-restraints excluded: chain C residue  236 VAL
Chi-restraints excluded: chain D residue  180 MET
Chi-restraints excluded: chain D residue  250 ILE
Chi-restraints excluded: chain D residue  321 ILE
Chi-restraints excluded: chain A residue   32 SER
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain B residue   24 ASN
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  206 THR
Chi-restraints excluded: chain B residue  216 THR
Chi-restraints excluded: chain B residue  224 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 62 optimal weight:    0.9980
   chunk 109 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 48 optimal weight:    4.9990
   chunk 103 optimal weight:    0.5980
   chunk 45 optimal weight:    0.6980
   chunk 72 optimal weight:    0.9980
   chunk 43 optimal weight:    0.5980
   chunk 65 optimal weight:    0.8980
   chunk 20 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** C  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 110 GLN
D 137 HIS
** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 280 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.156078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.118728 restraints weight = 13402.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.123099 restraints weight = 9039.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.124603 restraints weight = 5517.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.124666 restraints weight = 5277.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.125134 restraints weight = 4764.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7370
moved from start:          0.2203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  10222  Z= 0.172
  Angle     :  0.580   6.576  14072  Z= 0.320
  Chirality :  0.043   0.146   1619
  Planarity :  0.004   0.072   1591
  Dihedral  : 21.565 166.844   1939
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 12.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 12.98 %
    Favored  : 85.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.98 (0.24), residues: 1103
  helix:  0.56 (0.30), residues: 318
  sheet: -1.99 (0.27), residues: 317
  loop : -2.08 (0.25), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  70 
 TYR   0.012   0.002   TYR D  83 
 PHE   0.030   0.002   PHE B 214 
 TRP   0.007   0.001   TRP A  28 
 HIS   0.005   0.001   HIS C  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 (10220)
  covalent geometry    : angle       0.58003 (14068)
  SS BOND              : bond        0.00127 (    2)
  SS BOND              : angle       0.88610 (    4)
  hydrogen bonds       : bond        0.04223 (  449)
  hydrogen bonds       : angle       6.36867 ( 1230)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 129
  time to evaluate  : 0.293 
Fit side-chains
REVERT: C   53 ARG cc_start: 0.8055 (mtm180) cc_final: 0.7519 (mtm180)
REVERT: C   97 ASP cc_start: 0.5018 (p0) cc_final: 0.4118 (p0)
REVERT: C  214 PHE cc_start: 0.8627 (m-10) cc_final: 0.8230 (m-10)
REVERT: C  225 VAL cc_start: 0.8454 (t) cc_final: 0.8232 (p)
REVERT: B  131 GLN cc_start: 0.6824 (mm-40) cc_final: 0.6510 (mm-40)
REVERT: B  146 ARG cc_start: 0.7083 (ttt90) cc_final: 0.6840 (ttt90)
  outliers start: 15
  outliers final: 14
  residues processed: 139
  average time/residue: 0.0965
  time to fit residues: 18.9454
Evaluate side-chains
  137 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 123
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  236 VAL
Chi-restraints excluded: chain D residue   86 ASP
Chi-restraints excluded: chain D residue  110 GLN
Chi-restraints excluded: chain D residue  180 MET
Chi-restraints excluded: chain D residue  250 ILE
Chi-restraints excluded: chain D residue  321 ILE
Chi-restraints excluded: chain A residue   32 SER
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain B residue   24 ASN
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  206 THR
Chi-restraints excluded: chain B residue  216 THR
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain B residue  236 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 101 optimal weight:    2.9990
   chunk 60 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 102 optimal weight:    0.7980
   chunk 24 optimal weight:    0.6980
   chunk 46 optimal weight:    0.5980
   chunk 77 optimal weight:    0.6980
   chunk 48 optimal weight:    4.9990
   chunk 54 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
C  36 ASN
** C  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 107 ASN
D 110 GLN
D 137 HIS
** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.153980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.117096 restraints weight = 13341.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.120647 restraints weight = 7843.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.123055 restraints weight = 5527.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.124627 restraints weight = 4401.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.125687 restraints weight = 3780.645|
|-----------------------------------------------------------------------------|
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7338
moved from start:          0.2400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  10222  Z= 0.172
  Angle     :  0.577   6.211  14072  Z= 0.316
  Chirality :  0.043   0.146   1619
  Planarity :  0.004   0.072   1591
  Dihedral  : 21.681 166.531   1939
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 12.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 13.08 %
    Favored  : 84.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.87 (0.24), residues: 1103
  helix:  0.72 (0.30), residues: 318
  sheet: -2.03 (0.27), residues: 322
  loop : -1.98 (0.26), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  70 
 TYR   0.012   0.001   TYR D  83 
 PHE   0.031   0.002   PHE B 214 
 TRP   0.006   0.001   TRP A  28 
 HIS   0.005   0.001   HIS D 143 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 (10220)
  covalent geometry    : angle       0.57717 (14068)
  SS BOND              : bond        0.00130 (    2)
  SS BOND              : angle       0.90425 (    4)
  hydrogen bonds       : bond        0.04119 (  449)
  hydrogen bonds       : angle       6.29640 ( 1230)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 125
  time to evaluate  : 0.370 
Fit side-chains
REVERT: C   53 ARG cc_start: 0.8022 (mtm180) cc_final: 0.7629 (mtm180)
REVERT: C   97 ASP cc_start: 0.5088 (p0) cc_final: 0.4182 (p0)
REVERT: C  214 PHE cc_start: 0.8652 (m-10) cc_final: 0.8278 (m-10)
REVERT: C  225 VAL cc_start: 0.8439 (t) cc_final: 0.8235 (p)
REVERT: B  131 GLN cc_start: 0.6713 (mm-40) cc_final: 0.6431 (mm-40)
REVERT: B  146 ARG cc_start: 0.7047 (ttt90) cc_final: 0.6816 (ttt90)
  outliers start: 26
  outliers final: 21
  residues processed: 140
  average time/residue: 0.0860
  time to fit residues: 17.6215
Evaluate side-chains
  139 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 118
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  172 SER
Chi-restraints excluded: chain C residue  236 VAL
Chi-restraints excluded: chain C residue  243 ASP
Chi-restraints excluded: chain D residue   86 ASP
Chi-restraints excluded: chain D residue  110 GLN
Chi-restraints excluded: chain D residue  180 MET
Chi-restraints excluded: chain D residue  250 ILE
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   32 SER
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  199 MET
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain B residue   24 ASN
Chi-restraints excluded: chain B residue   81 CYS
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  206 THR
Chi-restraints excluded: chain B residue  216 THR
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain B residue  236 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 102 optimal weight:    0.8980
   chunk 115 optimal weight:    3.9990
   chunk 101 optimal weight:    3.9990
   chunk 108 optimal weight:    0.3980
   chunk 58 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 50 optimal weight:    0.8980
   chunk 32 optimal weight:    0.8980
   chunk 26 optimal weight:    3.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** C  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 110 GLN
D 137 HIS
** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.153366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.116344 restraints weight = 13502.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.119854 restraints weight = 7929.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.122215 restraints weight = 5629.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.123812 restraints weight = 4491.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.124869 restraints weight = 3852.979|
|-----------------------------------------------------------------------------|
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7354
moved from start:          0.2583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  10222  Z= 0.182
  Angle     :  0.585   6.576  14072  Z= 0.318
  Chirality :  0.043   0.143   1619
  Planarity :  0.004   0.072   1591
  Dihedral  : 21.652 166.143   1939
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 12.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 13.50 %
    Favored  : 83.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.82 (0.24), residues: 1103
  helix:  0.79 (0.30), residues: 320
  sheet: -2.06 (0.26), residues: 324
  loop : -1.91 (0.26), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  70 
 TYR   0.013   0.002   TYR D  83 
 PHE   0.032   0.002   PHE B 214 
 TRP   0.006   0.001   TRP D 274 
 HIS   0.005   0.001   HIS D 143 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 (10220)
  covalent geometry    : angle       0.58449 (14068)
  SS BOND              : bond        0.00141 (    2)
  SS BOND              : angle       0.92290 (    4)
  hydrogen bonds       : bond        0.04054 (  449)
  hydrogen bonds       : angle       6.25817 ( 1230)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 124
  time to evaluate  : 0.311 
Fit side-chains
REVERT: C   28 TRP cc_start: 0.8294 (m100) cc_final: 0.8026 (m100)
REVERT: C   53 ARG cc_start: 0.8007 (mtm180) cc_final: 0.7593 (mtm180)
REVERT: C  214 PHE cc_start: 0.8636 (m-10) cc_final: 0.8290 (m-10)
REVERT: C  225 VAL cc_start: 0.8442 (t) cc_final: 0.8237 (p)
REVERT: D  327 ARG cc_start: 0.6834 (OUTLIER) cc_final: 0.6485 (ptt180)
REVERT: A   40 MET cc_start: 0.7570 (ttt) cc_final: 0.7262 (ttm)
REVERT: B  131 GLN cc_start: 0.6640 (mm-40) cc_final: 0.6382 (mm-40)
REVERT: B  146 ARG cc_start: 0.7106 (ttt90) cc_final: 0.6879 (ttt90)
  outliers start: 30
  outliers final: 23
  residues processed: 143
  average time/residue: 0.0891
  time to fit residues: 18.3962
Evaluate side-chains
  144 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 120
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  172 SER
Chi-restraints excluded: chain C residue  236 VAL
Chi-restraints excluded: chain C residue  243 ASP
Chi-restraints excluded: chain D residue   86 ASP
Chi-restraints excluded: chain D residue  110 GLN
Chi-restraints excluded: chain D residue  180 MET
Chi-restraints excluded: chain D residue  250 ILE
Chi-restraints excluded: chain D residue  327 ARG
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   32 SER
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  199 MET
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain B residue   24 ASN
Chi-restraints excluded: chain B residue   81 CYS
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  206 THR
Chi-restraints excluded: chain B residue  216 THR
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain B residue  236 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   chunk 90 optimal weight:    0.1980
   chunk 21 optimal weight:    0.9980
   chunk 16 optimal weight:    0.5980
   chunk 94 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 46 optimal weight:    0.5980
   chunk 85 optimal weight:    3.9990
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** C  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 110 GLN
D 137 HIS
** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.153876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.117626 restraints weight = 13177.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.121098 restraints weight = 7625.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.123482 restraints weight = 5333.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.125147 restraints weight = 4202.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.126171 restraints weight = 3566.923|
|-----------------------------------------------------------------------------|
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7326
moved from start:          0.2665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  10222  Z= 0.158
  Angle     :  0.573   7.529  14072  Z= 0.310
  Chirality :  0.042   0.161   1619
  Planarity :  0.004   0.066   1591
  Dihedral  : 21.575 166.003   1939
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 12.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 14.75 %
    Favored  : 82.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.77 (0.24), residues: 1103
  helix:  0.83 (0.30), residues: 320
  sheet: -2.04 (0.27), residues: 316
  loop : -1.89 (0.25), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  70 
 TYR   0.011   0.001   TYR D  83 
 PHE   0.033   0.002   PHE B 214 
 TRP   0.010   0.001   TRP D 274 
 HIS   0.006   0.001   HIS D 143 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 (10220)
  covalent geometry    : angle       0.57248 (14068)
  SS BOND              : bond        0.00151 (    2)
  SS BOND              : angle       0.79995 (    4)
  hydrogen bonds       : bond        0.03869 (  449)
  hydrogen bonds       : angle       6.19524 ( 1230)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 130
  time to evaluate  : 0.313 
Fit side-chains
REVERT: C   28 TRP cc_start: 0.8285 (m100) cc_final: 0.8023 (m100)
REVERT: C   53 ARG cc_start: 0.8000 (mtm180) cc_final: 0.7606 (mtm180)
REVERT: C   97 ASP cc_start: 0.5293 (p0) cc_final: 0.4387 (p0)
REVERT: C  214 PHE cc_start: 0.8623 (m-10) cc_final: 0.8255 (m-10)
REVERT: D   74 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.7037 (mmt)
REVERT: D  182 CYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7761 (t)
REVERT: D  327 ARG cc_start: 0.6863 (OUTLIER) cc_final: 0.6521 (ptt180)
REVERT: A   40 MET cc_start: 0.7584 (ttt) cc_final: 0.7280 (ttm)
REVERT: B  131 GLN cc_start: 0.6539 (mm-40) cc_final: 0.6302 (mm-40)
  outliers start: 25
  outliers final: 18
  residues processed: 142
  average time/residue: 0.0952
  time to fit residues: 19.1270
Evaluate side-chains
  140 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 119
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  172 SER
Chi-restraints excluded: chain C residue  236 VAL
Chi-restraints excluded: chain D residue   74 MET
Chi-restraints excluded: chain D residue   86 ASP
Chi-restraints excluded: chain D residue  180 MET
Chi-restraints excluded: chain D residue  182 CYS
Chi-restraints excluded: chain D residue  250 ILE
Chi-restraints excluded: chain D residue  327 ARG
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue  199 MET
Chi-restraints excluded: chain B residue   24 ASN
Chi-restraints excluded: chain B residue   81 CYS
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  139 MET
Chi-restraints excluded: chain B residue  206 THR
Chi-restraints excluded: chain B residue  216 THR
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  236 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 90 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 96 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 58 optimal weight:    0.0770
   chunk 8 optimal weight:    0.9980
   chunk 77 optimal weight:    0.7980
   chunk 80 optimal weight:    0.4980
   chunk 7 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 103 optimal weight:    0.0980
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
** C  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 110 GLN
D 137 HIS
** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  44 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.154740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.118061 restraints weight = 13259.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.121570 restraints weight = 7750.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.123944 restraints weight = 5462.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.125522 restraints weight = 4356.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.126585 restraints weight = 3739.531|
|-----------------------------------------------------------------------------|
r_work (final): 0.3598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7316
moved from start:          0.2834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10222  Z= 0.143
  Angle     :  0.559   6.935  14072  Z= 0.303
  Chirality :  0.042   0.156   1619
  Planarity :  0.003   0.065   1591
  Dihedral  : 21.461 165.787   1939
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 11.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 15.78 %
    Favored  : 81.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.65 (0.24), residues: 1103
  helix:  0.96 (0.30), residues: 320
  sheet: -1.93 (0.27), residues: 316
  loop : -1.87 (0.25), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 146 
 TYR   0.010   0.001   TYR B 250 
 PHE   0.032   0.002   PHE B 214 
 TRP   0.010   0.001   TRP D 274 
 HIS   0.007   0.001   HIS C  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 (10220)
  covalent geometry    : angle       0.55913 (14068)
  SS BOND              : bond        0.00149 (    2)
  SS BOND              : angle       0.70324 (    4)
  hydrogen bonds       : bond        0.03659 (  449)
  hydrogen bonds       : angle       6.06517 ( 1230)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 126
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
REVERT: C   28 TRP cc_start: 0.8289 (m100) cc_final: 0.8023 (m100)
REVERT: C   53 ARG cc_start: 0.7974 (mtm180) cc_final: 0.7575 (mtm180)
REVERT: C   97 ASP cc_start: 0.5202 (p0) cc_final: 0.4347 (p0)
REVERT: C  214 PHE cc_start: 0.8606 (m-10) cc_final: 0.8271 (m-10)
REVERT: D   74 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.7090 (mmt)
REVERT: D  182 CYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7737 (t)
REVERT: D  327 ARG cc_start: 0.6899 (OUTLIER) cc_final: 0.6569 (ptt180)
REVERT: A   40 MET cc_start: 0.7557 (ttt) cc_final: 0.7266 (ttm)
REVERT: B   91 ARG cc_start: 0.6967 (mtt90) cc_final: 0.6754 (mtp180)
  outliers start: 25
  outliers final: 20
  residues processed: 141
  average time/residue: 0.1079
  time to fit residues: 21.4026
Evaluate side-chains
  143 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 120
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   20 LYS
Chi-restraints excluded: chain C residue  172 SER
Chi-restraints excluded: chain C residue  236 VAL
Chi-restraints excluded: chain D residue   74 MET
Chi-restraints excluded: chain D residue   86 ASP
Chi-restraints excluded: chain D residue  180 MET
Chi-restraints excluded: chain D residue  182 CYS
Chi-restraints excluded: chain D residue  250 ILE
Chi-restraints excluded: chain D residue  327 ARG
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   32 SER
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  199 MET
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  120 ASP
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  139 MET
Chi-restraints excluded: chain B residue  206 THR
Chi-restraints excluded: chain B residue  216 THR
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  236 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 50 optimal weight:    0.5980
   chunk 15 optimal weight:    2.9990
   chunk 76 optimal weight:    0.6980
   chunk 58 optimal weight:    2.9990
   chunk 60 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9990
   chunk 11 optimal weight:    0.7980
   chunk 73 optimal weight:    7.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** C  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 137 HIS
** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 204 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.152707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.115896 restraints weight = 13296.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.119340 restraints weight = 7858.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.121702 restraints weight = 5577.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.123246 restraints weight = 4461.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.124277 restraints weight = 3843.520|
|-----------------------------------------------------------------------------|
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7361
moved from start:          0.2936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  10222  Z= 0.185
  Angle     :  0.593   6.438  14072  Z= 0.319
  Chirality :  0.043   0.157   1619
  Planarity :  0.004   0.064   1591
  Dihedral  : 21.499 164.333   1939
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 12.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 15.16 %
    Favored  : 81.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.69 (0.24), residues: 1103
  helix:  0.90 (0.30), residues: 321
  sheet: -2.05 (0.26), residues: 321
  loop : -1.80 (0.26), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 146 
 TYR   0.013   0.002   TYR B 250 
 PHE   0.035   0.002   PHE B 214 
 TRP   0.010   0.002   TRP D 274 
 HIS   0.009   0.001   HIS C  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 (10220)
  covalent geometry    : angle       0.59256 (14068)
  SS BOND              : bond        0.00157 (    2)
  SS BOND              : angle       0.86721 (    4)
  hydrogen bonds       : bond        0.03853 (  449)
  hydrogen bonds       : angle       6.18245 ( 1230)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 122
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
REVERT: C   53 ARG cc_start: 0.7987 (mtm180) cc_final: 0.7556 (mtm180)
REVERT: C   97 ASP cc_start: 0.5421 (p0) cc_final: 0.4523 (p0)
REVERT: C  214 PHE cc_start: 0.8644 (m-10) cc_final: 0.8271 (m-10)
REVERT: D   74 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.6974 (mmt)
REVERT: D  327 ARG cc_start: 0.6867 (OUTLIER) cc_final: 0.6488 (ptt180)
REVERT: A   40 MET cc_start: 0.7641 (ttt) cc_final: 0.7350 (ttm)
REVERT: B  131 GLN cc_start: 0.6802 (mp10) cc_final: 0.6246 (mm-40)
  outliers start: 29
  outliers final: 20
  residues processed: 139
  average time/residue: 0.0996
  time to fit residues: 19.9684
Evaluate side-chains
  140 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 118
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   20 LYS
Chi-restraints excluded: chain C residue  172 SER
Chi-restraints excluded: chain C residue  236 VAL
Chi-restraints excluded: chain D residue   74 MET
Chi-restraints excluded: chain D residue   86 ASP
Chi-restraints excluded: chain D residue  180 MET
Chi-restraints excluded: chain D residue  250 ILE
Chi-restraints excluded: chain D residue  327 ARG
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   32 SER
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  199 MET
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain B residue   24 ASN
Chi-restraints excluded: chain B residue   81 CYS
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  206 THR
Chi-restraints excluded: chain B residue  216 THR
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  236 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 65 optimal weight:    0.6980
   chunk 39 optimal weight:    0.5980
   chunk 107 optimal weight:    0.9990
   chunk 9 optimal weight:    0.5980
   chunk 43 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9990
   chunk 36 optimal weight:    8.9990
   chunk 32 optimal weight:    0.9980
   chunk 97 optimal weight:    0.7980
   chunk 85 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** C  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 137 HIS
** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  44 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.155390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.117873 restraints weight = 13186.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.121461 restraints weight = 7746.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.123908 restraints weight = 5469.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.125560 restraints weight = 4366.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.126714 restraints weight = 3742.229|
|-----------------------------------------------------------------------------|
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7344
moved from start:          0.3032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10222  Z= 0.162
  Angle     :  0.577   6.511  14072  Z= 0.311
  Chirality :  0.043   0.149   1619
  Planarity :  0.004   0.063   1591
  Dihedral  : 21.390 162.144   1939
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 12.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 16.20 %
    Favored  : 81.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.67 (0.24), residues: 1103
  helix:  0.91 (0.30), residues: 322
  sheet: -2.00 (0.27), residues: 320
  loop : -1.81 (0.26), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 146 
 TYR   0.011   0.001   TYR B 250 
 PHE   0.035   0.002   PHE B 214 
 TRP   0.010   0.002   TRP D 274 
 HIS   0.007   0.001   HIS C  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 (10220)
  covalent geometry    : angle       0.57736 (14068)
  SS BOND              : bond        0.00148 (    2)
  SS BOND              : angle       0.79589 (    4)
  hydrogen bonds       : bond        0.03703 (  449)
  hydrogen bonds       : angle       6.12874 ( 1230)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 118
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
REVERT: C   53 ARG cc_start: 0.7951 (mtm180) cc_final: 0.7554 (mtm180)
REVERT: C   97 ASP cc_start: 0.5331 (p0) cc_final: 0.4471 (p0)
REVERT: C  214 PHE cc_start: 0.8638 (m-10) cc_final: 0.8256 (m-10)
REVERT: D   74 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.6976 (mmt)
REVERT: D  327 ARG cc_start: 0.6867 (OUTLIER) cc_final: 0.6494 (ptt180)
REVERT: A   40 MET cc_start: 0.7619 (ttt) cc_final: 0.7339 (ttm)
REVERT: B  131 GLN cc_start: 0.6783 (mp10) cc_final: 0.6178 (mm-40)
  outliers start: 23
  outliers final: 20
  residues processed: 132
  average time/residue: 0.1005
  time to fit residues: 18.9875
Evaluate side-chains
  139 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 117
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   20 LYS
Chi-restraints excluded: chain C residue  172 SER
Chi-restraints excluded: chain C residue  236 VAL
Chi-restraints excluded: chain D residue   74 MET
Chi-restraints excluded: chain D residue   86 ASP
Chi-restraints excluded: chain D residue  180 MET
Chi-restraints excluded: chain D residue  250 ILE
Chi-restraints excluded: chain D residue  327 ARG
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   32 SER
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  199 MET
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain B residue   24 ASN
Chi-restraints excluded: chain B residue   81 CYS
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  206 THR
Chi-restraints excluded: chain B residue  216 THR
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  236 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 84 optimal weight:    0.8980
   chunk 81 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9990
   chunk 36 optimal weight:    8.9990
   chunk 54 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** C  38 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 = 0.3936 r_free = 0.3936 target = 0.153760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.115968 restraints weight = 13367.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.119563 restraints weight = 7867.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.122033 restraints weight = 5580.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.123555 restraints weight = 4452.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.124723 restraints weight = 3847.596|
|-----------------------------------------------------------------------------|
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start:          0.3127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  10222  Z= 0.194
  Angle     :  0.604   6.368  14072  Z= 0.324
  Chirality :  0.043   0.144   1619
  Planarity :  0.004   0.062   1591
  Dihedral  : 21.432 160.165   1939
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 13.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 15.68 %
    Favored  : 81.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.72 (0.24), residues: 1103
  helix:  0.86 (0.29), residues: 322
  sheet: -2.10 (0.26), residues: 321
  loop : -1.79 (0.26), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 146 
 TYR   0.013   0.002   TYR B 250 
 PHE   0.037   0.002   PHE B 214 
 TRP   0.011   0.002   TRP D 274 
 HIS   0.007   0.001   HIS D 143 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 (10220)
  covalent geometry    : angle       0.60391 (14068)
  SS BOND              : bond        0.00178 (    2)
  SS BOND              : angle       0.93707 (    4)
  hydrogen bonds       : bond        0.03898 (  449)
  hydrogen bonds       : angle       6.25124 ( 1230)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1879.01 seconds
wall clock time: 33 minutes 15.03 seconds (1995.03 seconds total)