Starting phenix.real_space_refine
on Wed Sep 17 06:14:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6pwc_20505/09_2025/6pwc_20505.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6pwc_20505/09_2025/6pwc_20505.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6pwc_20505/09_2025/6pwc_20505.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6pwc_20505/09_2025/6pwc_20505.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6pwc_20505/09_2025/6pwc_20505.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6pwc_20505/09_2025/6pwc_20505.map"
  }
  resolution = 4.9
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      25      5.16       5
     C    3562      2.51       5
     N    1065      2.21       5
     O    1227      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  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: 5879
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "R"
      Number of atoms: 1824
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 323, 1824
          Classifications: {'peptide': 323}
          Incomplete info: {'truncation_to_alanine': 174}
          Link IDs: {'PTRANS': 10, 'TRANS': 312}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 779
          Unresolved non-hydrogen angles: 1003
          Unresolved non-hydrogen dihedrals: 677
          Unresolved non-hydrogen chiralities: 60
          Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 8, 'ASN:plan1': 13, 'TYR:plan': 14, 'ARG:plan': 15, 'GLN:plan1': 8, 'PHE:plan': 17, 'TRP:plan': 4, 'HIS:plan': 9}
          Unresolved non-hydrogen planarities: 475
    Chain: "B"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 27
          Classifications: {'peptide': 5}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 1, 'TRANS': 3}
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 17
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "A"
      Number of atoms: 1935
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 350, 1935
          Classifications: {'peptide': 350}
          Incomplete info: {'truncation_to_alanine': 206}
          Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 324}
          Unresolved non-hydrogen bonds: 863
          Unresolved non-hydrogen angles: 1078
          Unresolved non-hydrogen dihedrals: 721
          Unresolved non-hydrogen chiralities: 55
          Planarities with less than four sites: {'ARG:plan': 20, 'ASN:plan1': 14, 'TYR:plan': 11, 'ASP:plan': 21, 'PHE:plan': 12, 'HIS:plan': 8, 'GLU:plan': 24, 'GLN:plan1': 8}
          Unresolved non-hydrogen planarities: 522
    Chain: "H"
      Number of atoms: 1072
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1072
          Classifications: {'peptide': 194}
          Incomplete info: {'truncation_to_alanine': 88}
          Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 184}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 445
          Unresolved non-hydrogen angles: 580
          Unresolved non-hydrogen dihedrals: 405
          Unresolved non-hydrogen chiralities: 20
          Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 4, 'ARG:plan': 6, 'PHE:plan': 6, 'ASN:plan1': 7, 'TYR:plan': 14, 'HIS:plan': 3, 'TRP:plan': 5, 'ASP:plan': 6}
          Unresolved non-hydrogen planarities: 307
    Chain: "L"
      Number of atoms: 1021
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 183, 1021
          Classifications: {'peptide': 183}
          Incomplete info: {'truncation_to_alanine': 88}
          Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 172}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 411
          Unresolved non-hydrogen angles: 522
          Unresolved non-hydrogen dihedrals: 360
          Unresolved non-hydrogen chiralities: 18
          Planarities with less than four sites: {'ASP:plan': 8, 'GLN:plan1': 14, 'ARG:plan': 6, 'TRP:plan': 2, 'TYR:plan': 10, 'PHE:plan': 7, 'GLU:plan': 6, 'ASN:plan1': 3, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 278
  Time building chain proxies: 1.87, per 1000 atoms: 0.32
  Number of scatterers: 5879
  At special positions: 0
  Unit cell: (161.867, 106.193, 90.728, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      25     16.00
     O    1227      8.00
     N    1065      7.00
     C    3562      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 141 " - pdb=" SG  CYS R 224 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 279 " - pdb=" SG  CYS H  59 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  25 " - pdb=" SG  CYS H  99 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  24 " - pdb=" SG  CYS L  89 " 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: 0.50
  Conformation dependent library (CDL) restraints added in 410.6 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2000

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 17 sheets defined
      30.4% alpha, 29.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'R' and resid 59 through 91
    Processing helix  chain 'R' and resid 92 through 94
      No H-bonds generated for 'chain 'R' and resid 92 through 94'
    Processing helix  chain 'R' and resid 98 through 129
      Proline residue:  R 121  - end of helix
    Processing helix  chain 'R' and resid 137 through 172
    Processing helix  chain 'R' and resid 172 through 179
      removed outlier: 3.959A  pdb=" N   LYS R 177 " --> pdb=" O   PRO R 173 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 181 through 200
    Processing helix  chain 'R' and resid 201 through 205
    Processing helix  chain 'R' and resid 218 through 220
      No H-bonds generated for 'chain 'R' and resid 218 through 220'
    Processing helix  chain 'R' and resid 229 through 245
    Processing helix  chain 'R' and resid 245 through 269
      removed outlier: 3.694A  pdb=" N   VAL R 267 " --> pdb=" O   LEU R 263 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   ARG R 268 " --> pdb=" O   THR R 264 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 294 through 329
      removed outlier: 3.848A  pdb=" N   VAL R 309 " --> pdb=" O   LEU R 305 " (cutoff:3.500A)
      Proline residue:  R 318  - end of helix
      removed outlier: 4.197A  pdb=" N   ARG R 323 " --> pdb=" O   TYR R 319 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ILE R 329 " --> pdb=" O   MET R 325 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 335 through 368
      removed outlier: 4.160A  pdb=" N   ASN R 360 " --> pdb=" O   SER R 356 " (cutoff:3.500A)
      Proline residue:  R 361  - end of helix
    Processing helix  chain 'R' and resid 368 through 383
    Processing helix  chain 'A' and resid 65 through 72
    Processing helix  chain 'A' and resid 98 through 109
    Processing helix  chain 'A' and resid 278 through 282
    Processing helix  chain 'H' and resid 31 through 33
      No H-bonds generated for 'chain 'H' and resid 31 through 33'
    Processing helix  chain 'H' and resid 90 through 94
    Processing helix  chain 'H' and resid 166 through 168
      No H-bonds generated for 'chain 'H' and resid 166 through 168'
    Processing helix  chain 'L' and resid 80 through 84
      removed outlier: 3.775A  pdb=" N   PHE L  84 " --> pdb=" O   PRO L  81 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 122 through 127
    Processing helix  chain 'L' and resid 185 through 190
      removed outlier: 4.252A  pdb=" N   LYS L 189 " --> pdb=" O   ALA L 185 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'R' and resid 208 through 211
    Processing sheet with id=AA2, first strand: chain 'R' and resid 411 through 413
      removed outlier: 3.629A  pdb=" N   ASN R 411 " --> pdb=" O   LYS A  10 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   THR R 413 " --> pdb=" O   VAL A   8 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 26 through 29
      removed outlier: 5.898A  pdb=" N   PHE A  27 " --> pdb=" O   VAL A 171 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 75 through 77
      removed outlier: 4.036A  pdb=" N   PHE A  75 " --> pdb=" O   TYR A  63 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   VAL A  53 " --> pdb=" O   SER A  86 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 75 through 77
      removed outlier: 4.036A  pdb=" N   PHE A  75 " --> pdb=" O   TYR A  63 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 127 through 129
    Processing sheet with id=AA7, first strand: chain 'A' and resid 183 through 188
    Processing sheet with id=AA8, first strand: chain 'A' and resid 207 through 209
      removed outlier: 6.065A  pdb=" N   TYR A 208 " --> pdb=" O   MET A 352 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   TYR A 321 " --> pdb=" O   PHE A 349 " (cutoff:3.500A)
      removed outlier: 6.193A  pdb=" N   SER A 330 " --> pdb=" O   VAL A 228 " (cutoff:3.500A)
      removed outlier: 5.154A  pdb=" N   VAL A 228 " --> pdb=" O   SER A 330 " (cutoff:3.500A)
      removed outlier: 5.858A  pdb=" N   GLN A 237 " --> pdb=" O   PRO A 252 " (cutoff:3.500A)
      removed outlier: 7.379A  pdb=" N   ALA A 239 " --> pdb=" O   LYS A 250 " (cutoff:3.500A)
      removed outlier: 5.575A  pdb=" N   LYS A 250 " --> pdb=" O   ALA A 239 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 6 through 10
    Processing sheet with id=AB1, first strand: chain 'H' and resid 13 through 15
      removed outlier: 5.888A  pdb=" N   ARG H  41 " --> pdb=" O   TRP H  50 " (cutoff:3.500A)
      removed outlier: 5.788A  pdb=" N   TRP H  50 " --> pdb=" O   ARG H  41 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 13 through 15
    Processing sheet with id=AB3, first strand: chain 'H' and resid 130 through 133
      removed outlier: 5.927A  pdb=" N   TYR H 186 " --> pdb=" O   ASP H 154 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   SER H 187 " --> pdb=" O   VAL H 179 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   VAL H 179 " --> pdb=" O   SER H 187 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 161 through 164
    Processing sheet with id=AB5, first strand: chain 'H' and resid 173 through 175
    Processing sheet with id=AB6, first strand: chain 'L' and resid 5 through 8
    Processing sheet with id=AB7, first strand: chain 'L' and resid 11 through 14
      removed outlier: 6.236A  pdb=" N   LEU L  12 " --> pdb=" O   GLU L 106 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   GLN L  38 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
      removed outlier: 5.608A  pdb=" N   LEU L  47 " --> pdb=" O   GLN L  38 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'L' and resid 115 through 119
      removed outlier: 6.105A  pdb=" N   TYR L 174 " --> pdb=" O   ASN L 139 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   THR L 179 " --> pdb=" O   GLN L 161 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   ASN L 159 " --> pdb=" O   THR L 181 " (cutoff:3.500A)

    429 hydrogen bonds defined for protein.
    1182 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.04

  Time building geometry restraints manager: 0.66 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2088
        1.34 -     1.46: 1158
        1.46 -     1.58: 2664
        1.58 -     1.70: 0
        1.70 -     1.82: 25
  Bond restraints: 5935
  Sorted by residual:
  bond pdb=" C   LYS A 355 "
       pdb=" N   PRO A 356 "
    ideal  model  delta    sigma   weight residual
    1.341  1.376 -0.035 1.60e-02 3.91e+03 4.87e+00
  bond pdb=" C   MET R 120 "
       pdb=" N   PRO R 121 "
    ideal  model  delta    sigma   weight residual
    1.336  1.359 -0.023 1.20e-02 6.94e+03 3.52e+00
  bond pdb=" C   VAL R 201 "
       pdb=" N   PRO R 202 "
    ideal  model  delta    sigma   weight residual
    1.335  1.356 -0.022 1.19e-02 7.06e+03 3.35e+00
  bond pdb=" C   LEU R 317 "
       pdb=" N   PRO R 318 "
    ideal  model  delta    sigma   weight residual
    1.336  1.357 -0.022 1.25e-02 6.40e+03 2.98e+00
  bond pdb=" CA  VAL R 201 "
       pdb=" C   VAL R 201 "
    ideal  model  delta    sigma   weight residual
    1.523  1.537 -0.014 9.20e-03 1.18e+04 2.31e+00
  ... (remaining 5930 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.57: 8005
        1.57 -     3.14: 236
        3.14 -     4.70: 21
        4.70 -     6.27: 12
        6.27 -     7.84: 6
  Bond angle restraints: 8280
  Sorted by residual:
  angle pdb=" C   ALA R 200 "
        pdb=" N   VAL R 201 "
        pdb=" CA  VAL R 201 "
      ideal   model   delta    sigma   weight residual
     120.33  125.09   -4.76 8.00e-01 1.56e+00 3.54e+01
  angle pdb=" CA  VAL R 201 "
        pdb=" C   VAL R 201 "
        pdb=" N   PRO R 202 "
      ideal   model   delta    sigma   weight residual
     120.83  122.82   -1.99 6.10e-01 2.69e+00 1.07e+01
  angle pdb=" C   SER L  51 "
        pdb=" N   ALA L  52 "
        pdb=" CA  ALA L  52 "
      ideal   model   delta    sigma   weight residual
     121.54  127.59   -6.05 1.91e+00 2.74e-01 1.00e+01
  angle pdb=" CA  LYS A  95 "
        pdb=" C   LYS A  95 "
        pdb=" N   PRO A  96 "
      ideal   model   delta    sigma   weight residual
     118.44  123.01   -4.57 1.59e+00 3.96e-01 8.25e+00
  angle pdb=" CA  GLY A 316 "
        pdb=" C   GLY A 316 "
        pdb=" N   ILE A 317 "
      ideal   model   delta    sigma   weight residual
     114.62  118.23   -3.61 1.26e+00 6.30e-01 8.20e+00
  ... (remaining 8275 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.22: 3517
       12.22 -    24.43: 24
       24.43 -    36.65: 2
       36.65 -    48.87: 3
       48.87 -    61.08: 2
  Dihedral angle restraints: 3548
    sinusoidal: 501
      harmonic: 3047
  Sorted by residual:
  dihedral pdb=" CB  CYS R 141 "
           pdb=" SG  CYS R 141 "
           pdb=" SG  CYS R 224 "
           pdb=" CB  CYS R 224 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  154.08  -61.08     1      1.00e+01 1.00e-02 4.96e+01
  dihedral pdb=" CB  CYS A 279 "
           pdb=" SG  CYS A 279 "
           pdb=" SG  CYS H  59 "
           pdb=" CB  CYS H  59 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -32.21  -53.79     1      1.00e+01 1.00e-02 3.93e+01
  dihedral pdb=" CA  TRP H 113 "
           pdb=" C   TRP H 113 "
           pdb=" N   GLY H 114 "
           pdb=" CA  GLY H 114 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.97   21.03     0      5.00e+00 4.00e-02 1.77e+01
  ... (remaining 3545 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 765
       0.036 -    0.072: 268
       0.072 -    0.109: 88
       0.109 -    0.145: 48
       0.145 -    0.181: 3
  Chirality restraints: 1172
  Sorted by residual:
  chirality pdb=" CA  THR R 115 "
            pdb=" N   THR R 115 "
            pdb=" C   THR R 115 "
            pdb=" CB  THR R 115 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.34    0.18 2.00e-01 2.50e+01 8.21e-01
  chirality pdb=" CA  MET R 120 "
            pdb=" N   MET R 120 "
            pdb=" C   MET R 120 "
            pdb=" CB  MET R 120 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.18 2.00e-01 2.50e+01 7.69e-01
  chirality pdb=" CA  LEU R 317 "
            pdb=" N   LEU R 317 "
            pdb=" C   LEU R 317 "
            pdb=" CB  LEU R 317 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.77e-01
  ... (remaining 1169 not shown)

  Planarity restraints: 1111
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR R 225 "    0.030 5.00e-02 4.00e+02   4.60e-02 3.39e+00
        pdb=" N   PRO R 226 "   -0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO R 226 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO R 226 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL R 267 "    0.009 2.00e-02 2.50e+03   1.75e-02 3.06e+00
        pdb=" C   VAL R 267 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   VAL R 267 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ARG R 268 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR R 144 "    0.018 2.00e-02 2.50e+03   1.23e-02 3.03e+00
        pdb=" CG  TYR R 144 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD1 TYR R 144 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR R 144 "   -0.016 2.00e-02 2.50e+03
        pdb=" CE1 TYR R 144 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR R 144 "    0.015 2.00e-02 2.50e+03
        pdb=" CZ  TYR R 144 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR R 144 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1108 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.86: 1987
        2.86 -     3.37: 5096
        3.37 -     3.88: 8881
        3.88 -     4.39: 7784
        4.39 -     4.90: 15405
  Nonbonded interactions: 39153
  Sorted by model distance:
  nonbonded pdb=" O   ASN R 240 "
            pdb=" OG  SER R 244 "
     model   vdw
     2.345 3.040
  nonbonded pdb=" O   TYR R 354 "
            pdb=" OG1 THR R 358 "
     model   vdw
     2.376 3.040
  nonbonded pdb=" O   HIS H 210 "
            pdb=" N   ASN H 214 "
     model   vdw
     2.380 3.120
  nonbonded pdb=" O   ALA A 301 "
            pdb=" OH  TYR A 321 "
     model   vdw
     2.393 3.040
  nonbonded pdb=" O   ALA A 263 "
            pdb=" OG  SER A 266 "
     model   vdw
     2.401 3.040
  ... (remaining 39148 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.250
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.950
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6765
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      :  0.003   0.045   5939  Z= 0.180
  Angle     :  0.668   7.838   8288  Z= 0.392
  Chirality :  0.046   0.181   1172
  Planarity :  0.006   0.046   1111
  Dihedral  :  4.676  21.029   1536
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 2.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.91 %
    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: -0.09 (0.24), residues: 1031
  helix:  0.54 (0.27), residues: 265
  sheet:  0.29 (0.28), residues: 327
  loop : -0.60 (0.27), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG R 372 
 TYR   0.029   0.002   TYR R 344 
 PHE   0.002   0.000   PHE R  74 
 TRP   0.001   0.000   TRP R 193 
 HIS   0.007   0.004   HIS R 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 5935)
  covalent geometry    : angle       0.66740 ( 8280)
  SS BOND              : bond        0.00446 (    4)
  SS BOND              : angle       0.85865 (    8)
  hydrogen bonds       : bond        0.11431 (  419)
  hydrogen bonds       : angle       5.85626 ( 1182)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.285 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 30
  average time/residue: 0.0316
  time to fit residues: 2.0223
Evaluate side-chains
  19 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 49 optimal weight:   40.0000
   chunk 97 optimal weight:   10.0000
   chunk 53 optimal weight:   20.0000
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:   20.0000
   chunk 62 optimal weight:   50.0000
   chunk 51 optimal weight:   30.0000
   chunk 100 optimal weight:   30.0000
   chunk 38 optimal weight:    8.9990
   chunk 61 optimal weight:   10.0000
   overall best weight:    9.1996

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

Flipped N/Q/H residues before XYZ refinement:
R 104 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.038572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2607 r_free = 0.2607 target = 0.026594 restraints weight = 107194.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2607 r_free = 0.2607 target = 0.026594 restraints weight = 108807.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2607 r_free = 0.2607 target = 0.026594 restraints weight = 108808.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.2607 r_free = 0.2607 target = 0.026594 restraints weight = 108808.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2607 r_free = 0.2607 target = 0.026594 restraints weight = 108808.345|
|-----------------------------------------------------------------------------|
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5686
moved from start:          0.4432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.068   5939  Z= 0.298
  Angle     :  0.723   6.219   8288  Z= 0.427
  Chirality :  0.043   0.177   1172
  Planarity :  0.006   0.074   1111
  Dihedral  :  5.809  24.706   1048
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.91 %
    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:  0.14 (0.25), residues: 1031
  helix:  1.57 (0.29), residues: 276
  sheet: -0.67 (0.26), residues: 359
  loop : -0.01 (0.30), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.002   ARG R 372 
 TYR   0.022   0.002   TYR A 321 
 PHE   0.015   0.001   PHE A  80 
 TRP   0.003   0.000   TRP R 193 
 HIS   0.006   0.003   HIS R 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00509 ( 5935)
  covalent geometry    : angle       0.72270 ( 8280)
  SS BOND              : bond        0.00467 (    4)
  SS BOND              : angle       1.09152 (    8)
  hydrogen bonds       : bond        0.05176 (  419)
  hydrogen bonds       : angle       7.08298 ( 1182)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.242 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 20
  average time/residue: 0.0286
  time to fit residues: 1.3846
Evaluate side-chains
  14 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 74 optimal weight:    7.9990
   chunk 71 optimal weight:    4.9990
   chunk 80 optimal weight:   30.0000
   chunk 79 optimal weight:    4.9990
   chunk 12 optimal weight:   20.0000
   chunk 78 optimal weight:    4.9990
   chunk 21 optimal weight:    9.9990
   chunk 45 optimal weight:   30.0000
   chunk 32 optimal weight:   20.0000
   chunk 59 optimal weight:    5.9990
   chunk 33 optimal weight:    0.6980
   overall best weight:    4.3388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.039090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2618 r_free = 0.2618 target = 0.026881 restraints weight = 103163.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2618 r_free = 0.2618 target = 0.026874 restraints weight = 104039.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 14)----------------|
| r_work = 0.2618 r_free = 0.2618 target = 0.026873 restraints weight = 104390.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 15)----------------|
| r_work = 0.2618 r_free = 0.2618 target = 0.026873 restraints weight = 104402.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2618 r_free = 0.2618 target = 0.026873 restraints weight = 104402.421|
|-----------------------------------------------------------------------------|
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5535
moved from start:          0.4614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   5939  Z= 0.144
  Angle     :  0.492   6.896   8288  Z= 0.267
  Chirality :  0.040   0.147   1172
  Planarity :  0.004   0.060   1111
  Dihedral  :  4.272  17.146   1048
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.91 %
    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:  0.77 (0.26), residues: 1031
  helix:  2.59 (0.31), residues: 274
  sheet: -0.53 (0.27), residues: 337
  loop :  0.15 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.001   ARG R 372 
 TYR   0.013   0.001   TYR R 144 
 PHE   0.009   0.001   PHE A  80 
 TRP   0.002   0.000   TRP R 193 
 HIS   0.005   0.002   HIS R 300 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 5935)
  covalent geometry    : angle       0.49221 ( 8280)
  SS BOND              : bond        0.00297 (    4)
  SS BOND              : angle       0.62011 (    8)
  hydrogen bonds       : bond        0.03288 (  419)
  hydrogen bonds       : angle       5.43154 ( 1182)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  18 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.235 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 18
  average time/residue: 0.0289
  time to fit residues: 1.2771
Evaluate side-chains
  15 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 15
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 84 optimal weight:   40.0000
   chunk 22 optimal weight:   50.0000
   chunk 41 optimal weight:   10.0000
   chunk 97 optimal weight:   40.0000
   chunk 28 optimal weight:   30.0000
   chunk 65 optimal weight:   30.0000
   chunk 7 optimal weight:    8.9990
   chunk 46 optimal weight:   20.0000
   chunk 51 optimal weight:   10.0000
   chunk 52 optimal weight:    6.9990
   chunk 3 optimal weight:    9.9990
   overall best weight:    9.1994

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

Flipped N/Q/H residues before XYZ refinement:
R 300 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2818 r_free = 0.2818 target = 0.034395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2482 r_free = 0.2482 target = 0.023495 restraints weight = 112051.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2482 r_free = 0.2482 target = 0.023495 restraints weight = 111635.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2482 r_free = 0.2482 target = 0.023495 restraints weight = 111635.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.2482 r_free = 0.2482 target = 0.023495 restraints weight = 111635.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2482 r_free = 0.2482 target = 0.023495 restraints weight = 111635.997|
|-----------------------------------------------------------------------------|
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5775
moved from start:          0.7467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.083   5939  Z= 0.296
  Angle     :  0.713   6.187   8288  Z= 0.414
  Chirality :  0.043   0.165   1172
  Planarity :  0.005   0.050   1111
  Dihedral  :  6.109  24.960   1048
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 16.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.91 %
    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: -0.34 (0.26), residues: 1031
  helix:  1.99 (0.30), residues: 278
  sheet: -1.26 (0.27), residues: 336
  loop : -0.73 (0.29), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.003   ARG R 372 
 TYR   0.020   0.001   TYR R 144 
 PHE   0.013   0.001   PHE A   9 
 TRP   0.002   0.000   TRP R 193 
 HIS   0.010   0.004   HIS R 300 

Details of bonding type rmsd
  covalent geometry    : bond        0.00512 ( 5935)
  covalent geometry    : angle       0.71245 ( 8280)
  SS BOND              : bond        0.00527 (    4)
  SS BOND              : angle       0.92348 (    8)
  hydrogen bonds       : bond        0.05109 (  419)
  hydrogen bonds       : angle       7.43658 ( 1182)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 15
  time to evaluate  : 0.230 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 15
  average time/residue: 0.0249
  time to fit residues: 1.0462
Evaluate side-chains
  14 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 66 optimal weight:   30.0000
   chunk 36 optimal weight:    0.8980
   chunk 81 optimal weight:   10.0000
   chunk 53 optimal weight:   20.0000
   chunk 85 optimal weight:    9.9990
   chunk 38 optimal weight:    7.9990
   chunk 33 optimal weight:   20.0000
   chunk 88 optimal weight:   50.0000
   chunk 102 optimal weight:    0.9990
   chunk 16 optimal weight:   20.0000
   chunk 5 optimal weight:   10.0000
   overall best weight:    5.9790

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.034935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2496 r_free = 0.2496 target = 0.023711 restraints weight = 111688.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2497 r_free = 0.2497 target = 0.023737 restraints weight = 110550.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2497 r_free = 0.2497 target = 0.023737 restraints weight = 109494.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.2497 r_free = 0.2497 target = 0.023737 restraints weight = 109494.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2497 r_free = 0.2497 target = 0.023737 restraints weight = 109494.947|
|-----------------------------------------------------------------------------|
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5713
moved from start:          0.7572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5939  Z= 0.176
  Angle     :  0.538   7.511   8288  Z= 0.298
  Chirality :  0.040   0.151   1172
  Planarity :  0.004   0.047   1111
  Dihedral  :  5.051  22.239   1048
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.83 %
    Favored  : 99.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.91 %
    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:  0.01 (0.26), residues: 1031
  helix:  2.52 (0.31), residues: 278
  sheet: -1.31 (0.28), residues: 321
  loop : -0.51 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.002   ARG R 372 
 TYR   0.015   0.001   TYR R 144 
 PHE   0.014   0.001   PHE A   9 
 TRP   0.002   0.000   TRP R 193 
 HIS   0.004   0.001   HIS R 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 5935)
  covalent geometry    : angle       0.53718 ( 8280)
  SS BOND              : bond        0.00508 (    4)
  SS BOND              : angle       0.98989 (    8)
  hydrogen bonds       : bond        0.03599 (  419)
  hydrogen bonds       : angle       6.28124 ( 1182)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.218 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 16
  average time/residue: 0.0278
  time to fit residues: 1.1663
Evaluate side-chains
  14 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 29 optimal weight:    7.9990
   chunk 54 optimal weight:   20.0000
   chunk 48 optimal weight:    9.9990
   chunk 18 optimal weight:    7.9990
   chunk 4 optimal weight:   30.0000
   chunk 42 optimal weight:   10.0000
   chunk 21 optimal weight:    6.9990
   chunk 97 optimal weight:   50.0000
   chunk 53 optimal weight:   10.0000
   chunk 71 optimal weight:    2.9990
   overall best weight:    6.1990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2810 r_free = 0.2810 target = 0.034096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2478 r_free = 0.2478 target = 0.023293 restraints weight = 112175.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2479 r_free = 0.2479 target = 0.023305 restraints weight = 110020.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.2479 r_free = 0.2479 target = 0.023305 restraints weight = 109495.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.2479 r_free = 0.2479 target = 0.023305 restraints weight = 109489.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2479 r_free = 0.2479 target = 0.023305 restraints weight = 109489.576|
|-----------------------------------------------------------------------------|
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5740
moved from start:          0.8556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5939  Z= 0.184
  Angle     :  0.553   7.331   8288  Z= 0.308
  Chirality :  0.040   0.142   1172
  Planarity :  0.005   0.048   1111
  Dihedral  :  4.979  22.931   1048
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.83 %
    Favored  : 99.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.91 %
    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:  0.04 (0.27), residues: 1031
  helix:  3.00 (0.30), residues: 273
  sheet: -1.50 (0.28), residues: 316
  loop : -0.63 (0.30), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 372 
 TYR   0.016   0.001   TYR R 144 
 PHE   0.010   0.001   PHE A   9 
 TRP   0.002   0.000   TRP R 193 
 HIS   0.004   0.002   HIS R 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 5935)
  covalent geometry    : angle       0.55169 ( 8280)
  SS BOND              : bond        0.00511 (    4)
  SS BOND              : angle       1.17641 (    8)
  hydrogen bonds       : bond        0.03737 (  419)
  hydrogen bonds       : angle       6.16157 ( 1182)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 15
  time to evaluate  : 0.202 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 15
  average time/residue: 0.0292
  time to fit residues: 1.1052
Evaluate side-chains
  14 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 42 optimal weight:    5.9990
   chunk 77 optimal weight:   20.0000
   chunk 90 optimal weight:   10.0000
   chunk 49 optimal weight:    1.9990
   chunk 29 optimal weight:    8.9990
   chunk 97 optimal weight:   30.0000
   chunk 98 optimal weight:   40.0000
   chunk 84 optimal weight:    3.9990
   chunk 96 optimal weight:    0.0170
   chunk 19 optimal weight:   50.0000
   chunk 15 optimal weight:   50.0000
   overall best weight:    4.2026

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2828 r_free = 0.2828 target = 0.034564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2492 r_free = 0.2492 target = 0.023570 restraints weight = 110751.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2494 r_free = 0.2494 target = 0.023625 restraints weight = 108830.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 14)----------------|
| r_work = 0.2494 r_free = 0.2494 target = 0.023626 restraints weight = 106655.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.2494 r_free = 0.2494 target = 0.023626 restraints weight = 106623.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2494 r_free = 0.2494 target = 0.023626 restraints weight = 106623.094|
|-----------------------------------------------------------------------------|
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5709
moved from start:          0.8615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   5939  Z= 0.132
  Angle     :  0.493   7.306   8288  Z= 0.268
  Chirality :  0.040   0.142   1172
  Planarity :  0.004   0.046   1111
  Dihedral  :  4.571  21.895   1048
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.91 %
    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:  0.19 (0.27), residues: 1031
  helix:  3.04 (0.31), residues: 280
  sheet: -1.44 (0.28), residues: 316
  loop : -0.50 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 372 
 TYR   0.015   0.001   TYR R 144 
 PHE   0.012   0.001   PHE A   9 
 TRP   0.002   0.000   TRP R 193 
 HIS   0.003   0.001   HIS R 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 5935)
  covalent geometry    : angle       0.49285 ( 8280)
  SS BOND              : bond        0.00424 (    4)
  SS BOND              : angle       0.78634 (    8)
  hydrogen bonds       : bond        0.03190 (  419)
  hydrogen bonds       : angle       5.72505 ( 1182)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 15
  time to evaluate  : 0.150 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 15
  average time/residue: 0.0275
  time to fit residues: 1.1383
Evaluate side-chains
  14 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 58 optimal weight:   40.0000
   chunk 45 optimal weight:   50.0000
   chunk 32 optimal weight:    4.9990
   chunk 48 optimal weight:    7.9990
   chunk 90 optimal weight:    0.9990
   chunk 43 optimal weight:   20.0000
   chunk 39 optimal weight:   30.0000
   chunk 76 optimal weight:   20.0000
   chunk 67 optimal weight:   40.0000
   chunk 98 optimal weight:   30.0000
   chunk 26 optimal weight:    0.0570
   overall best weight:    6.8108

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.033498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2458 r_free = 0.2458 target = 0.022878 restraints weight = 113241.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2458 r_free = 0.2458 target = 0.022878 restraints weight = 110300.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2458 r_free = 0.2458 target = 0.022878 restraints weight = 110300.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.2458 r_free = 0.2458 target = 0.022878 restraints weight = 110300.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2458 r_free = 0.2458 target = 0.022878 restraints weight = 110300.826|
|-----------------------------------------------------------------------------|
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5742
moved from start:          0.9427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5939  Z= 0.191
  Angle     :  0.563   7.325   8288  Z= 0.315
  Chirality :  0.041   0.143   1172
  Planarity :  0.005   0.046   1111
  Dihedral  :  5.171  23.929   1048
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 12.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.98 %
    Favored  : 93.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.83 %
    Favored  : 99.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.91 %
    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: -0.08 (0.27), residues: 1031
  helix:  3.01 (0.30), residues: 274
  sheet: -1.58 (0.28), residues: 304
  loop : -0.80 (0.30), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.001   ARG R 372 
 TYR   0.016   0.001   TYR R 144 
 PHE   0.013   0.001   PHE A   9 
 TRP   0.002   0.000   TRP R 193 
 HIS   0.002   0.001   HIS R 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 5935)
  covalent geometry    : angle       0.56267 ( 8280)
  SS BOND              : bond        0.00603 (    4)
  SS BOND              : angle       0.93972 (    8)
  hydrogen bonds       : bond        0.03964 (  419)
  hydrogen bonds       : angle       6.43707 ( 1182)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 15
  time to evaluate  : 0.221 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 15
  average time/residue: 0.0251
  time to fit residues: 0.9482
Evaluate side-chains
  14 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 18 optimal weight:    8.9990
   chunk 86 optimal weight:    3.9990
   chunk 95 optimal weight:    0.0570
   chunk 96 optimal weight:    9.9990
   chunk 66 optimal weight:   30.0000
   chunk 4 optimal weight:   20.0000
   chunk 87 optimal weight:   10.0000
   chunk 67 optimal weight:   40.0000
   chunk 69 optimal weight:    5.9990
   chunk 41 optimal weight:   10.0000
   overall best weight:    4.2106

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.034013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2476 r_free = 0.2476 target = 0.023178 restraints weight = 111437.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2477 r_free = 0.2477 target = 0.023207 restraints weight = 108699.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 18)----------------|
| r_work = 0.2478 r_free = 0.2478 target = 0.023222 restraints weight = 107333.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 16)----------------|
| r_work = 0.2480 r_free = 0.2480 target = 0.023276 restraints weight = 106662.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2482 r_free = 0.2482 target = 0.023326 restraints weight = 104382.380|
|-----------------------------------------------------------------------------|
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5703
moved from start:          0.9414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   5939  Z= 0.131
  Angle     :  0.491   7.397   8288  Z= 0.267
  Chirality :  0.040   0.141   1172
  Planarity :  0.004   0.048   1111
  Dihedral  :  4.570  21.880   1048
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.91 %
    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:  0.16 (0.28), residues: 1031
  helix:  3.15 (0.31), residues: 280
  sheet: -1.40 (0.28), residues: 307
  loop : -0.71 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG R 372 
 TYR   0.014   0.001   TYR R 144 
 PHE   0.010   0.001   PHE A   9 
 TRP   0.002   0.000   TRP R 193 
 HIS   0.003   0.001   HIS R 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 5935)
  covalent geometry    : angle       0.49099 ( 8280)
  SS BOND              : bond        0.00401 (    4)
  SS BOND              : angle       0.67129 (    8)
  hydrogen bonds       : bond        0.03173 (  419)
  hydrogen bonds       : angle       5.75689 ( 1182)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 15
  time to evaluate  : 0.228 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 15
  average time/residue: 0.0253
  time to fit residues: 1.0160
Evaluate side-chains
  14 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 36 optimal weight:    0.0050
   chunk 25 optimal weight:   20.0000
   chunk 44 optimal weight:   20.0000
   chunk 84 optimal weight:    7.9990
   chunk 63 optimal weight:    6.9990
   chunk 38 optimal weight:   20.0000
   chunk 7 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 50 optimal weight:    8.9990
   chunk 59 optimal weight:    8.9990
   chunk 55 optimal weight:   10.0000
   overall best weight:    3.7600

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.034080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2478 r_free = 0.2478 target = 0.023160 restraints weight = 111327.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2478 r_free = 0.2478 target = 0.023160 restraints weight = 108774.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2478 r_free = 0.2478 target = 0.023160 restraints weight = 108774.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.2478 r_free = 0.2478 target = 0.023160 restraints weight = 108774.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2478 r_free = 0.2478 target = 0.023160 restraints weight = 108774.231|
|-----------------------------------------------------------------------------|
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5708
moved from start:          0.9619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   5939  Z= 0.125
  Angle     :  0.473   7.866   8288  Z= 0.254
  Chirality :  0.039   0.136   1172
  Planarity :  0.004   0.047   1111
  Dihedral  :  4.213  20.756   1048
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.91 %
    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:  0.38 (0.28), residues: 1031
  helix:  3.40 (0.31), residues: 280
  sheet: -1.27 (0.29), residues: 308
  loop : -0.62 (0.31), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.001   ARG R 372 
 TYR   0.013   0.001   TYR R 144 
 PHE   0.008   0.001   PHE A   9 
 TRP   0.001   0.000   TRP R 193 
 HIS   0.003   0.001   HIS R 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 ( 5935)
  covalent geometry    : angle       0.47276 ( 8280)
  SS BOND              : bond        0.00428 (    4)
  SS BOND              : angle       0.79253 (    8)
  hydrogen bonds       : bond        0.03000 (  419)
  hydrogen bonds       : angle       5.33139 ( 1182)

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.264 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 16
  average time/residue: 0.0256
  time to fit residues: 1.0423
Evaluate side-chains
  15 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 15
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 2 optimal weight:    6.9990
   chunk 80 optimal weight:    0.2980
   chunk 86 optimal weight:    5.9990
   chunk 97 optimal weight:   30.0000
   chunk 84 optimal weight:    0.5980
   chunk 101 optimal weight:    7.9990
   chunk 61 optimal weight:   30.0000
   chunk 96 optimal weight:    0.6980
   chunk 74 optimal weight:   20.0000
   chunk 95 optimal weight:    8.9990
   chunk 98 optimal weight:   10.0000
   overall best weight:    2.9184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.034286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2485 r_free = 0.2485 target = 0.023289 restraints weight = 110206.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2487 r_free = 0.2487 target = 0.023342 restraints weight = 108014.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2487 r_free = 0.2487 target = 0.023342 restraints weight = 105578.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.2487 r_free = 0.2487 target = 0.023342 restraints weight = 105578.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2487 r_free = 0.2487 target = 0.023342 restraints weight = 105578.206|
|-----------------------------------------------------------------------------|
r_work (final): 0.3005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5689
moved from start:          0.9648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   5939  Z= 0.108
  Angle     :  0.465   7.738   8288  Z= 0.247
  Chirality :  0.039   0.141   1172
  Planarity :  0.004   0.047   1111
  Dihedral  :  4.074  19.873   1048
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.91 %
    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:  0.48 (0.28), residues: 1031
  helix:  3.46 (0.31), residues: 280
  sheet: -1.16 (0.30), residues: 299
  loop : -0.60 (0.31), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 372 
 TYR   0.011   0.001   TYR R 144 
 PHE   0.008   0.001   PHE A   9 
 TRP   0.001   0.000   TRP R 193 
 HIS   0.003   0.001   HIS R 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00193 ( 5935)
  covalent geometry    : angle       0.46344 ( 8280)
  SS BOND              : bond        0.00301 (    4)
  SS BOND              : angle       1.25253 (    8)
  hydrogen bonds       : bond        0.02804 (  419)
  hydrogen bonds       : angle       5.16305 ( 1182)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1051.68 seconds
wall clock time: 18 minutes 50.29 seconds (1130.29 seconds total)