Starting phenix.real_space_refine
on Wed Feb 12 06:53:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8r9z_19017/02_2025/8r9z_19017.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8r9z_19017/02_2025/8r9z_19017.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8r9z_19017/02_2025/8r9z_19017.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8r9z_19017/02_2025/8r9z_19017.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8r9z_19017/02_2025/8r9z_19017.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8r9z_19017/02_2025/8r9z_19017.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.012
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      35      5.16       5
     C    4682      2.51       5
     N    1246      2.21       5
     O    1478      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7441
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 889
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 889
          Classifications: {'peptide': 114}
          Link IDs: {'PTRANS': 1, 'TRANS': 112}
    Chain: "B"
      Number of atoms: 1614
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1614
          Classifications: {'peptide': 218}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 13, 'TRANS': 204}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1623
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 209, 1623
          Classifications: {'peptide': 209}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 197}
    Chain: "H"
      Number of atoms: 1654
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1654
          Classifications: {'peptide': 219}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 207}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 1619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1619
          Classifications: {'peptide': 212}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 198}
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 4.99, per 1000 atoms: 0.67
  Number of scatterers: 7441
  At special positions: 0
  Unit cell: (73.9731, 105.12, 145.026, 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      35     16.00
     O    1478      8.00
     N    1246      7.00
     C    4682      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=11, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 335 " - pdb=" SG  CYS A 378 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 349 " - pdb=" SG  CYS A 352 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 361 " - pdb=" SG  CYS A 386 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 150 " - pdb=" SG  CYS B 206 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  23 " - pdb=" SG  CYS C  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 134 " - pdb=" SG  CYS C 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 148 " - pdb=" SG  CYS H 204 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 134 " - pdb=" SG  CYS L 194 " 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
  Links applied
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
    NAG-ASN
      " NAG A 501 " - " ASN A 331 "
      " NAG D   1 " - " ASN A 311 "
  Time building additional restraints: 1.75
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1800

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 24 sheets defined
      6.4% alpha, 49.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 364 through 371
      removed outlier: 4.801A  pdb=" N   ASN A 369 " --> pdb=" O   SER A 366 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   GLY A 371 " --> pdb=" O   VAL A 368 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 87 through 91
      removed outlier: 3.707A  pdb=" N   THR B  91 " --> pdb=" O   SER B  88 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 121 through 128
    Processing helix  chain 'C' and resid 183 through 188
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.700A  pdb=" N   TYR H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.634A  pdb=" N   THR H  91 " --> pdb=" O   ALA H  88 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 164 through 166
      No H-bonds generated for 'chain 'H' and resid 164 through 166'
    Processing helix  chain 'H' and resid 195 through 198
      removed outlier: 4.319A  pdb=" N   GLY H 198 " --> pdb=" O   SER H 195 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 195 through 198'
    Processing helix  chain 'L' and resid 79 through 83
      removed outlier: 3.687A  pdb=" N   VAL L  83 " --> pdb=" O   PRO L  80 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 121 through 127
    Processing helix  chain 'L' and resid 183 through 188
      removed outlier: 3.523A  pdb=" N   LYS L 188 " --> pdb=" O   ALA L 184 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 306 through 310
      removed outlier: 6.154A  pdb=" N   GLU A 306 " --> pdb=" O   ARG A 342 " (cutoff:3.500A)
      removed outlier: 7.284A  pdb=" N   GLU A 344 " --> pdb=" O   GLU A 306 " (cutoff:3.500A)
      removed outlier: 5.926A  pdb=" N   VAL A 308 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 333 through 335
      removed outlier: 8.393A  pdb=" N   GLN A 376 " --> pdb=" O   GLN A 412 " (cutoff:3.500A)
      removed outlier: 9.189A  pdb=" N   GLN A 412 " --> pdb=" O   GLN A 376 " (cutoff:3.500A)
      removed outlier: 11.233A  pdb=" N   CYS A 378 " --> pdb=" O   GLU A 410 " (cutoff:3.500A)
      removed outlier: 11.234A  pdb=" N   GLU A 410 " --> pdb=" O   CYS A 378 " (cutoff:3.500A)
      removed outlier: 11.798A  pdb=" N   SER A 380 " --> pdb=" O   ALA A 408 " (cutoff:3.500A)
      removed outlier: 10.484A  pdb=" N   ALA A 408 " --> pdb=" O   SER A 380 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 313 through 316
      removed outlier: 6.870A  pdb=" N   SER A 313 " --> pdb=" O   ASP A 324 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 6
    Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12
      removed outlier: 6.581A  pdb=" N   ARG B  38 " --> pdb=" O   TRP B  47 " (cutoff:3.500A)
      removed outlier: 5.316A  pdb=" N   TRP B  47 " --> pdb=" O   ARG B  38 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   THR B  57 " --> pdb=" O   ILE B  52 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 12
      removed outlier: 3.641A  pdb=" N   ILE B 112 " --> pdb=" O   ARG B  98 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 130 through 134
      removed outlier: 3.549A  pdb=" N   GLY B 149 " --> pdb=" O   LEU B 134 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   SER B 190 " --> pdb=" O   CYS B 150 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   TYR B 186 " --> pdb=" O   ASP B 154 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 130 through 134
      removed outlier: 3.549A  pdb=" N   GLY B 149 " --> pdb=" O   LEU B 134 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   SER B 190 " --> pdb=" O   CYS B 150 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   TYR B 186 " --> pdb=" O   ASP B 154 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 161 through 164
    Processing sheet with id=AB1, first strand: chain 'C' and resid 5 through 7
      removed outlier: 4.119A  pdb=" N   GLU C  70 " --> pdb=" O   SER C  67 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 13
      removed outlier: 6.631A  pdb=" N   LEU C  33 " --> pdb=" O   TYR C  49 " (cutoff:3.500A)
      removed outlier: 4.585A  pdb=" N   TYR C  49 " --> pdb=" O   LEU C  33 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   TRP C  35 " --> pdb=" O   LEU C  47 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 13
      removed outlier: 3.849A  pdb=" N   THR C  97 " --> pdb=" O   GLN C  90 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 114 through 118
      removed outlier: 6.355A  pdb=" N   TYR C 173 " --> pdb=" O   ASN C 138 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 153 through 154
      removed outlier: 3.649A  pdb=" N   CYS C 194 " --> pdb=" O   LYS C 207 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'H' and resid 3 through 7
      removed outlier: 3.653A  pdb=" N   VAL H   5 " --> pdb=" O   ALA H  23 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'H' and resid 11 through 12
      removed outlier: 6.640A  pdb=" N   MET H  34 " --> pdb=" O   VAL H  50 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   VAL H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'H' and resid 11 through 12
    Processing sheet with id=AB9, first strand: chain 'H' and resid 129 through 131
      removed outlier: 5.781A  pdb=" N   LEU H 149 " --> pdb=" O   SER H 188 " (cutoff:3.500A)
      removed outlier: 7.507A  pdb=" N   SER H 188 " --> pdb=" O   LEU H 149 " (cutoff:3.500A)
      removed outlier: 4.933A  pdb=" N   LYS H 151 " --> pdb=" O   LEU H 186 " (cutoff:3.500A)
      removed outlier: 5.575A  pdb=" N   LEU H 186 " --> pdb=" O   LYS H 151 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'H' and resid 143 through 145
    Processing sheet with id=AC2, first strand: chain 'H' and resid 158 through 162
      removed outlier: 4.604A  pdb=" N   TYR H 202 " --> pdb=" O   VAL H 219 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'L' and resid 4 through 7
      removed outlier: 3.832A  pdb=" N   ASP L  70 " --> pdb=" O   SER L  67 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'L' and resid 10 through 13
      removed outlier: 6.657A  pdb=" N   LEU L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
      removed outlier: 4.617A  pdb=" N   TYR L  49 " --> pdb=" O   LEU L  33 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'L' and resid 114 through 118
      removed outlier: 3.705A  pdb=" N   VAL L 133 " --> pdb=" O   PHE L 118 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   TYR L 173 " --> pdb=" O   ASN L 138 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'L' and resid 145 through 150
      removed outlier: 4.309A  pdb=" N   LYS L 145 " --> pdb=" O   THR L 197 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   THR L 197 " --> pdb=" O   LYS L 145 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   ALA L 193 " --> pdb=" O   LYS L 149 " (cutoff:3.500A)

    311 hydrogen bonds defined for protein.
    762 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: 2.56

  Time building geometry restraints manager: 2.05 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2374
        1.35 -     1.47: 2001
        1.47 -     1.60: 3183
        1.60 -     1.72: 0
        1.72 -     1.85: 48
  Bond restraints: 7606
  Sorted by residual:
  bond pdb=" C1  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.431 -0.025 2.00e-02 2.50e+03 1.62e+00
  bond pdb=" C1  NAG A 501 "
       pdb=" O5  NAG A 501 "
    ideal  model  delta    sigma   weight residual
    1.406  1.431 -0.025 2.00e-02 2.50e+03 1.61e+00
  bond pdb=" CB  CYS A 335 "
       pdb=" SG  CYS A 335 "
    ideal  model  delta    sigma   weight residual
    1.808  1.850 -0.042 3.30e-02 9.18e+02 1.59e+00
  bond pdb=" C5  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.413  1.435 -0.022 2.00e-02 2.50e+03 1.23e+00
  bond pdb=" C5  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.413  1.435 -0.022 2.00e-02 2.50e+03 1.22e+00
  ... (remaining 7601 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.40: 10246
        2.40 -     4.80: 87
        4.80 -     7.21: 12
        7.21 -     9.61: 1
        9.61 -    12.01: 1
  Bond angle restraints: 10347
  Sorted by residual:
  angle pdb=" CA  CYS A 378 "
        pdb=" CB  CYS A 378 "
        pdb=" SG  CYS A 378 "
      ideal   model   delta    sigma   weight residual
     114.40  122.57   -8.17 2.30e+00 1.89e-01 1.26e+01
  angle pdb=" CA  LEU B 200 "
        pdb=" CB  LEU B 200 "
        pdb=" CG  LEU B 200 "
      ideal   model   delta    sigma   weight residual
     116.30  128.31  -12.01 3.50e+00 8.16e-02 1.18e+01
  angle pdb=" N   VAL L 150 "
        pdb=" CA  VAL L 150 "
        pdb=" C   VAL L 150 "
      ideal   model   delta    sigma   weight residual
     106.21  109.65   -3.44 1.07e+00 8.73e-01 1.03e+01
  angle pdb=" C   VAL L 150 "
        pdb=" N   ASP L 151 "
        pdb=" CA  ASP L 151 "
      ideal   model   delta    sigma   weight residual
     121.54  127.53   -5.99 1.91e+00 2.74e-01 9.84e+00
  angle pdb=" C   LYS H 151 "
        pdb=" N   ASP H 152 "
        pdb=" CA  ASP H 152 "
      ideal   model   delta    sigma   weight residual
     121.26  125.93   -4.67 1.59e+00 3.96e-01 8.64e+00
  ... (remaining 10342 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.79: 4181
       16.79 -    33.58: 322
       33.58 -    50.36: 63
       50.36 -    67.15: 18
       67.15 -    83.94: 11
  Dihedral angle restraints: 4595
    sinusoidal: 1790
      harmonic: 2805
  Sorted by residual:
  dihedral pdb=" CB  CYS H 148 "
           pdb=" SG  CYS H 148 "
           pdb=" SG  CYS H 204 "
           pdb=" CB  CYS H 204 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  153.27  -60.27     1      1.00e+01 1.00e-02 4.84e+01
  dihedral pdb=" CB  CYS A 335 "
           pdb=" SG  CYS A 335 "
           pdb=" SG  CYS A 378 "
           pdb=" CB  CYS A 378 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   47.21   45.79     1      1.00e+01 1.00e-02 2.91e+01
  dihedral pdb=" CB  CYS B 150 "
           pdb=" SG  CYS B 150 "
           pdb=" SG  CYS B 206 "
           pdb=" CB  CYS B 206 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  138.25  -45.25     1      1.00e+01 1.00e-02 2.84e+01
  ... (remaining 4592 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 852
       0.040 -    0.080: 211
       0.080 -    0.120: 115
       0.120 -    0.160: 12
       0.160 -    0.200: 1
  Chirality restraints: 1191
  Sorted by residual:
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN A 311 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.20   -0.20 2.00e-01 2.50e+01 1.00e+00
  chirality pdb=" CA  ILE C  48 "
            pdb=" N   ILE C  48 "
            pdb=" C   ILE C  48 "
            pdb=" CB  ILE C  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.92e-01
  chirality pdb=" CA  ILE B  52 "
            pdb=" N   ILE B  52 "
            pdb=" C   ILE B  52 "
            pdb=" CB  ILE B  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.84e-01
  ... (remaining 1188 not shown)

  Planarity restraints: 1316
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 194 "    0.029 5.00e-02 4.00e+02   4.37e-02 3.06e+00
        pdb=" N   PRO B 195 "   -0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO B 195 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 195 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN L  79 "   -0.022 5.00e-02 4.00e+02   3.29e-02 1.74e+00
        pdb=" N   PRO L  80 "    0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO L  80 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO L  80 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN C 166 "    0.006 2.00e-02 2.50e+03   1.22e-02 1.48e+00
        pdb=" C   GLN C 166 "   -0.021 2.00e-02 2.50e+03
        pdb=" O   GLN C 166 "    0.008 2.00e-02 2.50e+03
        pdb=" N   ASP C 167 "    0.007 2.00e-02 2.50e+03
  ... (remaining 1313 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 1929
        2.80 -     3.33: 6285
        3.33 -     3.85: 11995
        3.85 -     4.38: 14282
        4.38 -     4.90: 25642
  Nonbonded interactions: 60133
  Sorted by model distance:
  nonbonded pdb=" OG  SER C 121 "
            pdb=" OE1 GLU C 123 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" O   ALA L  25 "
            pdb=" OG1 THR L  69 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" O   ASP C  82 "
            pdb=" OH  TYR C  86 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" O   TYR C 186 "
            pdb=" OH  TYR C 192 "
     model   vdw
     2.307 3.040
  nonbonded pdb=" OE1 GLN B  62 "
            pdb=" NH1 ARG B  65 "
     model   vdw
     2.310 3.120
  ... (remaining 60128 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.010
  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:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     21.810
  Find NCS groups from input model:        0.130
  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:11.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8567
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   0.042   7606  Z= 0.190
  Angle     :  0.568  12.009  10347  Z= 0.290
  Chirality :  0.044   0.200   1191
  Planarity :  0.004   0.044   1314
  Dihedral  : 13.351  83.940   2762
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.20 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.29), residues: 958
  helix: -1.80 (0.81), residues: 30
  sheet:  0.45 (0.25), residues: 463
  loop :  0.00 (0.33), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  94 
 HIS   0.003   0.001   HIS C 198 
 PHE   0.008   0.001   PHE L  71 
 TYR   0.012   0.001   TYR L 140 
 ARG   0.001   0.000   ARG H 105 

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.972 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  355 ASN cc_start: 0.8692 (m-40) cc_final: 0.8467 (p0)
REVERT: B   43 GLN cc_start: 0.8994 (mm110) cc_final: 0.8781 (mm110)
REVERT: H   12 VAL cc_start: 0.9025 (p) cc_final: 0.8761 (m)
REVERT: H   89 GLU cc_start: 0.8450 (pm20) cc_final: 0.8175 (pm20)
REVERT: L   17 ASP cc_start: 0.8309 (m-30) cc_final: 0.8089 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 1.5191
  time to fit residues: 200.3928
Evaluate side-chains
  88 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.801 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 79 optimal weight:    4.9990
   chunk 71 optimal weight:    8.9990
   chunk 39 optimal weight:    3.9990
   chunk 24 optimal weight:    0.4980
   chunk 48 optimal weight:    2.9990
   chunk 38 optimal weight:    0.5980
   chunk 73 optimal weight:    3.9990
   chunk 28 optimal weight:    0.8980
   chunk 44 optimal weight:    2.9990
   chunk 54 optimal weight:    4.9990
   chunk 85 optimal weight:    4.9990
   overall best weight:    1.5984

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

Flipped N/Q/H residues before XYZ refinement:
A 412 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.081777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.067530 restraints weight = 18031.699|
|-----------------------------------------------------------------------------|
r_work (start): 0.3094 rms_B_bonded: 2.90
r_work: 0.2988 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.1612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044   7606  Z= 0.370
  Angle     :  0.693   9.485  10347  Z= 0.363
  Chirality :  0.048   0.184   1191
  Planarity :  0.005   0.036   1314
  Dihedral  :  5.436  50.569   1104
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 10.06 %
    Favored  : 88.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.20 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.19 (0.29), residues: 958
  helix: -1.70 (0.86), residues: 31
  sheet:  0.52 (0.24), residues: 467
  loop : -0.04 (0.32), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  36 
 HIS   0.004   0.001   HIS B 174 
 PHE   0.014   0.002   PHE B 156 
 TYR   0.014   0.001   TYR L 140 
 ARG   0.006   0.001   ARG L 142 

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.795 
Fit side-chains
   revert: symmetry clash
REVERT: B   43 GLN cc_start: 0.9176 (mm110) cc_final: 0.8877 (mm110)
REVERT: B  222 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7356 (pm20)
REVERT: C   18 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8211 (ttm110)
REVERT: C  123 GLU cc_start: 0.7874 (mp0) cc_final: 0.7649 (mp0)
REVERT: H   89 GLU cc_start: 0.8848 (pm20) cc_final: 0.8413 (pm20)
REVERT: H  103 MET cc_start: 0.8845 (mtt) cc_final: 0.8403 (mtt)
REVERT: L    4 MET cc_start: 0.9388 (OUTLIER) cc_final: 0.8970 (mmm)
REVERT: L   17 ASP cc_start: 0.8331 (m-30) cc_final: 0.8040 (m-30)
REVERT: L  142 ARG cc_start: 0.8487 (ttt-90) cc_final: 0.8144 (tmt90)
  outliers start: 13
  outliers final: 3
  residues processed: 92
  average time/residue: 1.5663
  time to fit residues: 151.1731
Evaluate side-chains
  83 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 77
  time to evaluate  : 0.877 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  222 GLU
Chi-restraints excluded: chain C residue   18 ARG
Chi-restraints excluded: chain L residue    4 MET
Chi-restraints excluded: chain L residue  122 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 65 optimal weight:    0.5980
   chunk 64 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 67 optimal weight:    0.5980
   chunk 29 optimal weight:    1.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
A 355 ASN
A 370 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.082196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.067653 restraints weight = 17976.204|
|-----------------------------------------------------------------------------|
r_work (start): 0.3071 rms_B_bonded: 3.00
r_work: 0.2966 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
moved from start:          0.1792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   7606  Z= 0.265
  Angle     :  0.628   8.435  10347  Z= 0.329
  Chirality :  0.046   0.182   1191
  Planarity :  0.004   0.036   1314
  Dihedral  :  5.337  50.735   1104
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 13.53 %
    Favored  : 84.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.20 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.29), residues: 958
  helix: -1.46 (0.89), residues: 31
  sheet:  0.55 (0.24), residues: 466
  loop :  0.01 (0.32), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  94 
 HIS   0.003   0.001   HIS C 198 
 PHE   0.012   0.001   PHE H 154 
 TYR   0.013   0.001   TYR L 140 
 ARG   0.006   0.001   ARG C  54 

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 0.901 
Fit side-chains
   revert: symmetry clash
REVERT: B   29 PHE cc_start: 0.8945 (m-80) cc_final: 0.8699 (m-80)
REVERT: B   43 GLN cc_start: 0.9204 (mm110) cc_final: 0.8884 (mm110)
REVERT: B  207 ASN cc_start: 0.8507 (m-40) cc_final: 0.8281 (m-40)
REVERT: B  222 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7294 (pm20)
REVERT: C   18 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8266 (ttm110)
REVERT: C  123 GLU cc_start: 0.7863 (mp0) cc_final: 0.7568 (mp0)
REVERT: H   89 GLU cc_start: 0.8850 (pm20) cc_final: 0.8364 (pm20)
REVERT: L    4 MET cc_start: 0.9371 (OUTLIER) cc_final: 0.8821 (mmm)
REVERT: L   17 ASP cc_start: 0.8349 (m-30) cc_final: 0.8030 (m-30)
REVERT: L  142 ARG cc_start: 0.8542 (ttt-90) cc_final: 0.8265 (tmt90)
REVERT: L  145 LYS cc_start: 0.8193 (pttt) cc_final: 0.7962 (ptmm)
REVERT: L  187 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8340 (mm-30)
  outliers start: 13
  outliers final: 5
  residues processed: 92
  average time/residue: 1.4794
  time to fit residues: 142.9641
Evaluate side-chains
  84 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.901 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain B residue   73 ASP
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  222 GLU
Chi-restraints excluded: chain C residue   18 ARG
Chi-restraints excluded: chain L residue    4 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 36 optimal weight:    0.7980
   chunk 8 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 55 optimal weight:    0.5980
   chunk 4 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 72 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9990
   chunk 50 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 355 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.081607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.067597 restraints weight = 17880.484|
|-----------------------------------------------------------------------------|
r_work (start): 0.3085 rms_B_bonded: 2.90
r_work: 0.2981 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.1950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7606  Z= 0.223
  Angle     :  0.607   7.844  10347  Z= 0.316
  Chirality :  0.045   0.181   1191
  Planarity :  0.004   0.042   1314
  Dihedral  :  5.261  51.140   1104
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 14.13 %
    Favored  : 83.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.20 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.28 (0.29), residues: 958
  helix: -1.44 (0.87), residues: 31
  sheet:  0.56 (0.24), residues: 460
  loop :  0.03 (0.32), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C  94 
 HIS   0.003   0.001   HIS C 198 
 PHE   0.011   0.001   PHE H 154 
 TYR   0.015   0.001   TYR A 334 
 ARG   0.009   0.001   ARG L  24 

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 83
  time to evaluate  : 0.899 
Fit side-chains
   revert: symmetry clash
REVERT: B   29 PHE cc_start: 0.8945 (m-80) cc_final: 0.8718 (m-80)
REVERT: B   43 GLN cc_start: 0.9188 (mm110) cc_final: 0.8883 (mm110)
REVERT: B  222 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7268 (pm20)
REVERT: C  187 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8413 (mp0)
REVERT: H   89 GLU cc_start: 0.8833 (pm20) cc_final: 0.8452 (pm20)
REVERT: L    4 MET cc_start: 0.9352 (OUTLIER) cc_final: 0.8831 (mmm)
REVERT: L   17 ASP cc_start: 0.8343 (m-30) cc_final: 0.8038 (m-30)
REVERT: L  142 ARG cc_start: 0.8513 (ttt-90) cc_final: 0.8292 (tmt90)
REVERT: L  165 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8413 (mm-30)
REVERT: L  187 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8325 (mm-30)
  outliers start: 18
  outliers final: 6
  residues processed: 95
  average time/residue: 1.4618
  time to fit residues: 146.0161
Evaluate side-chains
  89 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.899 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  222 GLU
Chi-restraints excluded: chain C residue  181 LEU
Chi-restraints excluded: chain C residue  187 GLU
Chi-restraints excluded: chain L residue    4 MET
Chi-restraints excluded: chain L residue  165 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 31 optimal weight:    0.9980
   chunk 23 optimal weight:    3.9990
   chunk 30 optimal weight:    5.9990
   chunk 8 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0670
   chunk 91 optimal weight:    6.9990
   chunk 3 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    1.1722

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

Flipped N/Q/H residues before XYZ refinement:
A 355 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.081880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.067462 restraints weight = 18059.631|
|-----------------------------------------------------------------------------|
r_work (start): 0.3067 rms_B_bonded: 2.98
r_work: 0.2961 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.2100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   7606  Z= 0.283
  Angle     :  0.624   7.874  10347  Z= 0.325
  Chirality :  0.046   0.185   1191
  Planarity :  0.004   0.046   1314
  Dihedral  :  5.295  50.464   1104
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 15.09 %
    Favored  : 82.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.20 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.28), residues: 958
  helix: -1.48 (0.86), residues: 31
  sheet:  0.52 (0.24), residues: 466
  loop : -0.00 (0.32), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C  94 
 HIS   0.003   0.001   HIS C 198 
 PHE   0.013   0.001   PHE H 154 
 TYR   0.014   0.001   TYR L 140 
 ARG   0.011   0.001   ARG L  24 

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 84
  time to evaluate  : 0.933 
Fit side-chains
   revert: symmetry clash
REVERT: B   29 PHE cc_start: 0.8974 (m-80) cc_final: 0.8752 (m-80)
REVERT: B   43 GLN cc_start: 0.9199 (mm110) cc_final: 0.8870 (mm110)
REVERT: B  207 ASN cc_start: 0.8414 (m-40) cc_final: 0.8138 (m-40)
REVERT: B  208 VAL cc_start: 0.8653 (t) cc_final: 0.8416 (m)
REVERT: B  222 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7402 (pm20)
REVERT: C  187 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8434 (mp0)
REVERT: H   89 GLU cc_start: 0.8834 (pm20) cc_final: 0.8395 (pm20)
REVERT: L    4 MET cc_start: 0.9366 (OUTLIER) cc_final: 0.8827 (mmm)
REVERT: L   17 ASP cc_start: 0.8325 (m-30) cc_final: 0.8048 (m-30)
REVERT: L   24 ARG cc_start: 0.8317 (mtp-110) cc_final: 0.7887 (ttm-80)
REVERT: L   81 GLU cc_start: 0.9012 (mp0) cc_final: 0.8740 (pm20)
REVERT: L  142 ARG cc_start: 0.8582 (ttt-90) cc_final: 0.8366 (tmt90)
REVERT: L  165 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8437 (mm-30)
REVERT: L  187 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8350 (mm-30)
  outliers start: 19
  outliers final: 8
  residues processed: 97
  average time/residue: 1.3124
  time to fit residues: 134.6558
Evaluate side-chains
  90 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 78
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  222 GLU
Chi-restraints excluded: chain C residue   13 VAL
Chi-restraints excluded: chain C residue  181 LEU
Chi-restraints excluded: chain C residue  187 GLU
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain L residue    4 MET
Chi-restraints excluded: chain L residue  165 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 74 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 27 optimal weight:    4.9990
   chunk 46 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 52 optimal weight:    1.9990
   chunk 13 optimal weight:    5.9990
   chunk 4 optimal weight:    0.4980
   chunk 40 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
A 355 ASN
H 179 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.080043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.065918 restraints weight = 18184.281|
|-----------------------------------------------------------------------------|
r_work (start): 0.3051 rms_B_bonded: 2.93
r_work: 0.2945 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8505
moved from start:          0.2184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   7606  Z= 0.344
  Angle     :  0.656   9.795  10347  Z= 0.342
  Chirality :  0.047   0.192   1191
  Planarity :  0.004   0.036   1314
  Dihedral  :  5.417  49.827   1104
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 15.09 %
    Favored  : 81.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.20 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.28), residues: 958
  helix: -1.47 (0.86), residues: 31
  sheet:  0.51 (0.24), residues: 466
  loop : -0.08 (0.32), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C  94 
 HIS   0.003   0.001   HIS C 198 
 PHE   0.015   0.001   PHE H 154 
 TYR   0.019   0.002   TYR B  80 
 ARG   0.007   0.001   ARG C  54 

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 81
  time to evaluate  : 0.891 
Fit side-chains
   revert: symmetry clash
REVERT: B   29 PHE cc_start: 0.8970 (m-80) cc_final: 0.8769 (m-80)
REVERT: B   43 GLN cc_start: 0.9199 (mm110) cc_final: 0.8871 (mm110)
REVERT: C  187 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8432 (mp0)
REVERT: H   89 GLU cc_start: 0.8815 (pm20) cc_final: 0.8327 (pm20)
REVERT: L    4 MET cc_start: 0.9353 (OUTLIER) cc_final: 0.8857 (mmm)
REVERT: L   17 ASP cc_start: 0.8309 (m-30) cc_final: 0.8021 (m-30)
REVERT: L   24 ARG cc_start: 0.8353 (mtp-110) cc_final: 0.7985 (mtp-110)
REVERT: L   81 GLU cc_start: 0.8998 (mp0) cc_final: 0.8740 (pm20)
REVERT: L  129 THR cc_start: 0.8227 (OUTLIER) cc_final: 0.7990 (p)
REVERT: L  187 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8369 (mm-30)
  outliers start: 27
  outliers final: 12
  residues processed: 100
  average time/residue: 1.3804
  time to fit residues: 145.5617
Evaluate side-chains
  90 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 75
  time to evaluate  : 0.825 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  222 GLU
Chi-restraints excluded: chain C residue   13 VAL
Chi-restraints excluded: chain C residue  180 THR
Chi-restraints excluded: chain C residue  181 LEU
Chi-restraints excluded: chain C residue  187 GLU
Chi-restraints excluded: chain C residue  197 THR
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue  205 ASN
Chi-restraints excluded: chain L residue    4 MET
Chi-restraints excluded: chain L residue  129 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 62 optimal weight:    0.9990
   chunk 90 optimal weight:    3.9990
   chunk 72 optimal weight:    6.9990
   chunk 52 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 93 optimal weight:    2.9990
   chunk 92 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
A 355 ASN
H 179 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.079818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.065819 restraints weight = 17994.786|
|-----------------------------------------------------------------------------|
r_work (start): 0.3050 rms_B_bonded: 2.89
r_work: 0.2944 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2831 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.2831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8589
moved from start:          0.2271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   7606  Z= 0.358
  Angle     :  0.673   9.656  10347  Z= 0.351
  Chirality :  0.047   0.194   1191
  Planarity :  0.004   0.035   1314
  Dihedral  :  5.489  49.754   1104
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 16.65 %
    Favored  : 81.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.20 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.28), residues: 958
  helix: -1.49 (0.86), residues: 31
  sheet:  0.46 (0.24), residues: 466
  loop : -0.12 (0.31), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C  94 
 HIS   0.004   0.001   HIS C 198 
 PHE   0.015   0.002   PHE H 154 
 TYR   0.015   0.002   TYR L 140 
 ARG   0.008   0.001   ARG C  54 

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 75
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
REVERT: B   29 PHE cc_start: 0.9063 (m-80) cc_final: 0.8836 (m-80)
REVERT: B   43 GLN cc_start: 0.9257 (mm110) cc_final: 0.8960 (mm110)
REVERT: C  187 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8459 (mp0)
REVERT: H   89 GLU cc_start: 0.8952 (pm20) cc_final: 0.8440 (pm20)
REVERT: L    4 MET cc_start: 0.9431 (OUTLIER) cc_final: 0.8905 (mmm)
REVERT: L   17 ASP cc_start: 0.8458 (m-30) cc_final: 0.8159 (m-30)
REVERT: L   24 ARG cc_start: 0.8446 (mtp-110) cc_final: 0.8080 (mtp-110)
REVERT: L   81 GLU cc_start: 0.9065 (mp0) cc_final: 0.8797 (pm20)
REVERT: L  129 THR cc_start: 0.8231 (OUTLIER) cc_final: 0.7953 (p)
REVERT: L  187 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8445 (mm-30)
  outliers start: 19
  outliers final: 12
  residues processed: 89
  average time/residue: 1.4705
  time to fit residues: 137.8204
Evaluate side-chains
  87 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 72
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  222 GLU
Chi-restraints excluded: chain C residue   13 VAL
Chi-restraints excluded: chain C residue  181 LEU
Chi-restraints excluded: chain C residue  187 GLU
Chi-restraints excluded: chain C residue  197 THR
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  205 ASN
Chi-restraints excluded: chain L residue    4 MET
Chi-restraints excluded: chain L residue  129 THR
Chi-restraints excluded: chain L residue  134 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 67 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9980
   chunk 49 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 54 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9980
   chunk 92 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
A 355 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.080898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.066912 restraints weight = 18034.066|
|-----------------------------------------------------------------------------|
r_work (start): 0.3072 rms_B_bonded: 2.90
r_work: 0.2966 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.2287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   7606  Z= 0.245
  Angle     :  0.634   8.804  10347  Z= 0.330
  Chirality :  0.045   0.189   1191
  Planarity :  0.004   0.034   1314
  Dihedral  :  5.370  51.025   1104
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 16.77 %
    Favored  : 80.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.20 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.19 (0.28), residues: 958
  helix: -1.30 (0.88), residues: 31
  sheet:  0.52 (0.24), residues: 467
  loop : -0.08 (0.32), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 164 
 HIS   0.003   0.001   HIS C 198 
 PHE   0.013   0.001   PHE H 154 
 TYR   0.021   0.001   TYR A 334 
 ARG   0.008   0.001   ARG H  16 

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 80
  time to evaluate  : 0.806 
Fit side-chains
   revert: symmetry clash
REVERT: B   43 GLN cc_start: 0.9165 (mm110) cc_final: 0.8893 (mm110)
REVERT: C  187 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8419 (mp0)
REVERT: H   89 GLU cc_start: 0.8786 (pm20) cc_final: 0.8294 (pm20)
REVERT: L    4 MET cc_start: 0.9349 (OUTLIER) cc_final: 0.8808 (mmm)
REVERT: L   17 ASP cc_start: 0.8318 (m-30) cc_final: 0.8025 (m-30)
REVERT: L   24 ARG cc_start: 0.8333 (mtp-110) cc_final: 0.7903 (mtp-110)
REVERT: L   81 GLU cc_start: 0.9034 (mp0) cc_final: 0.8818 (pm20)
REVERT: L  129 THR cc_start: 0.8215 (OUTLIER) cc_final: 0.7972 (p)
REVERT: L  187 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8282 (mm-30)
  outliers start: 21
  outliers final: 14
  residues processed: 96
  average time/residue: 1.3107
  time to fit residues: 132.7619
Evaluate side-chains
  93 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 76
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain C residue   13 VAL
Chi-restraints excluded: chain C residue  180 THR
Chi-restraints excluded: chain C residue  181 LEU
Chi-restraints excluded: chain C residue  187 GLU
Chi-restraints excluded: chain C residue  197 THR
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  205 ASN
Chi-restraints excluded: chain L residue    4 MET
Chi-restraints excluded: chain L residue  129 THR
Chi-restraints excluded: chain L residue  134 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 81 optimal weight:    2.9990
   chunk 76 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9980
   chunk 16 optimal weight:    0.2980
   chunk 29 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   chunk 54 optimal weight:    4.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 355 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.081503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.067503 restraints weight = 18050.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.3087 rms_B_bonded: 2.93
r_work: 0.2980 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8469
moved from start:          0.2336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7606  Z= 0.219
  Angle     :  0.628   8.386  10347  Z= 0.327
  Chirality :  0.045   0.187   1191
  Planarity :  0.004   0.035   1314
  Dihedral  :  5.265  51.625   1104
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 17.37 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.20 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.28), residues: 958
  helix: -1.36 (0.85), residues: 31
  sheet:  0.58 (0.24), residues: 467
  loop : -0.04 (0.32), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 164 
 HIS   0.003   0.001   HIS C 198 
 PHE   0.010   0.001   PHE H 154 
 TYR   0.014   0.001   TYR L 140 
 ARG   0.007   0.001   ARG C  54 

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 82
  time to evaluate  : 0.923 
Fit side-chains
   revert: symmetry clash
REVERT: B   43 GLN cc_start: 0.9157 (mm110) cc_final: 0.8856 (mm110)
REVERT: H   89 GLU cc_start: 0.8777 (pm20) cc_final: 0.8275 (pm20)
REVERT: L    4 MET cc_start: 0.9368 (OUTLIER) cc_final: 0.8838 (mmm)
REVERT: L   17 ASP cc_start: 0.8315 (m-30) cc_final: 0.8061 (m-30)
REVERT: L   24 ARG cc_start: 0.8361 (mtp-110) cc_final: 0.7941 (mtp-110)
REVERT: L  187 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8309 (mm-30)
  outliers start: 19
  outliers final: 11
  residues processed: 97
  average time/residue: 1.3299
  time to fit residues: 136.2079
Evaluate side-chains
  87 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 0.831 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain C residue   13 VAL
Chi-restraints excluded: chain C residue  181 LEU
Chi-restraints excluded: chain C residue  197 THR
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  205 ASN
Chi-restraints excluded: chain L residue    4 MET
Chi-restraints excluded: chain L residue  134 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 88 optimal weight:    0.0670
   chunk 38 optimal weight:    4.9990
   chunk 19 optimal weight:    0.7980
   chunk 15 optimal weight:    2.9990
   chunk 93 optimal weight:    0.8980
   chunk 86 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.7318

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

Flipped N/Q/H residues before XYZ refinement:
A 355 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.081656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.067718 restraints weight = 18052.500|
|-----------------------------------------------------------------------------|
r_work (start): 0.3089 rms_B_bonded: 2.90
r_work: 0.2983 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
moved from start:          0.2381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7606  Z= 0.218
  Angle     :  0.646   8.148  10347  Z= 0.337
  Chirality :  0.045   0.188   1191
  Planarity :  0.004   0.035   1314
  Dihedral  :  5.232  51.808   1104
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 17.84 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.20 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.28), residues: 958
  helix: -1.33 (0.85), residues: 31
  sheet:  0.60 (0.24), residues: 467
  loop : -0.01 (0.32), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 113 
 HIS   0.003   0.001   HIS C 198 
 PHE   0.011   0.001   PHE H 154 
 TYR   0.025   0.001   TYR A 334 
 ARG   0.007   0.001   ARG C  54 

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 75
  time to evaluate  : 0.905 
Fit side-chains
   revert: symmetry clash
REVERT: B   43 GLN cc_start: 0.9184 (mm110) cc_final: 0.8878 (mm110)
REVERT: H   89 GLU cc_start: 0.8778 (pm20) cc_final: 0.8289 (pm20)
REVERT: L    4 MET cc_start: 0.9374 (OUTLIER) cc_final: 0.8842 (mmm)
REVERT: L   17 ASP cc_start: 0.8321 (m-30) cc_final: 0.8022 (m-30)
REVERT: L   24 ARG cc_start: 0.8361 (mtp-110) cc_final: 0.7941 (mtp-110)
REVERT: L  187 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8339 (mm-30)
  outliers start: 15
  outliers final: 14
  residues processed: 86
  average time/residue: 1.4015
  time to fit residues: 127.0606
Evaluate side-chains
  87 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 72
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain C residue   13 VAL
Chi-restraints excluded: chain C residue  181 LEU
Chi-restraints excluded: chain C residue  197 THR
Chi-restraints excluded: chain H residue    3 GLN
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  205 ASN
Chi-restraints excluded: chain L residue    1 ASP
Chi-restraints excluded: chain L residue    4 MET
Chi-restraints excluded: chain L residue  134 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 41 optimal weight:    0.4980
   chunk 4 optimal weight:    4.9990
   chunk 79 optimal weight:    4.9990
   chunk 0 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   chunk 23 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9980
   chunk 55 optimal weight:    3.9990
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
A 355 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.080921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.067060 restraints weight = 17973.681|
|-----------------------------------------------------------------------------|
r_work (start): 0.3077 rms_B_bonded: 2.89
r_work: 0.2971 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8477
moved from start:          0.2394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7606  Z= 0.271
  Angle     :  0.652   8.392  10347  Z= 0.340
  Chirality :  0.046   0.190   1191
  Planarity :  0.004   0.035   1314
  Dihedral  :  5.264  51.370   1104
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 17.84 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.20 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.28), residues: 958
  helix: -1.35 (0.85), residues: 31
  sheet:  0.55 (0.24), residues: 469
  loop : -0.06 (0.32), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 113 
 HIS   0.003   0.001   HIS C 198 
 PHE   0.012   0.001   PHE H 154 
 TYR   0.013   0.001   TYR L 140 
 ARG   0.007   0.001   ARG C  54 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4466.29 seconds
wall clock time: 79 minutes 53.77 seconds (4793.77 seconds total)