Starting phenix.real_space_refine
on Wed Feb 12 15:24:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d2t_27149/02_2025/8d2t_27149.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d2t_27149/02_2025/8d2t_27149.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8d2t_27149/02_2025/8d2t_27149.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d2t_27149/02_2025/8d2t_27149.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d2t_27149/02_2025/8d2t_27149.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d2t_27149/02_2025/8d2t_27149.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.042
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1606 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      33      5.16       5
     C    4322      2.51       5
     N    1015      2.21       5
     O    1239      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6609
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3413
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 460, 3380
          Classifications: {'peptide': 460}
          Incomplete info: {'truncation_to_alanine': 61}
          Link IDs: {'PTRANS': 20, 'TRANS': 439}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 222
          Unresolved non-hydrogen angles: 269
          Unresolved non-hydrogen dihedrals: 183
          Unresolved non-hydrogen chiralities: 11
          Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 134
      Conformer: "B"
        Number of residues, atoms: 460, 3380
          Classifications: {'peptide': 460}
          Incomplete info: {'truncation_to_alanine': 61}
          Link IDs: {'PTRANS': 20, 'TRANS': 439}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 222
          Unresolved non-hydrogen angles: 269
          Unresolved non-hydrogen dihedrals: 183
          Unresolved non-hydrogen chiralities: 11
          Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 134
          bond proxies already assigned to first conformer: 3432
    Chain: "B"
      Number of atoms: 1395
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1395
          Classifications: {'peptide': 201}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 14, 'TRANS': 186}
          Unresolved non-hydrogen bonds: 58
          Unresolved non-hydrogen angles: 71
          Unresolved non-hydrogen dihedrals: 45
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 33
    Chain: "C"
      Number of atoms: 1412
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 203, 1412
          Classifications: {'peptide': 203}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 12, 'TRANS': 190}
          Unresolved non-hydrogen bonds: 41
          Unresolved non-hydrogen angles: 49
          Unresolved non-hydrogen dihedrals: 33
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 18
    Chain: "A"
      Number of atoms: 350
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 9, 315
          Unusual residues: {'LMT': 9}
          Classifications: {'undetermined': 9}
          Link IDs: {None: 8}
      Conformer: "B"
        Number of residues, atoms: 9, 315
          Unusual residues: {'LMT': 9}
          Classifications: {'undetermined': 9}
          Link IDs: {None: 8}
          bond proxies already assigned to first conformer: 288
    Chain: "B"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 35
          Unusual residues: {'LMT': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}
  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N  AARG A 323 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A 323 " occ=0.50
    residue:
      pdb=" N  APHE A 396 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE A 396 " occ=0.50
    residue:
      pdb=" N  APHE A 449 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE A 449 " occ=0.50
    residue:
      pdb=" C1 ALMT A 603 " occ=0.50
      ... (68 atoms not shown)
      pdb=" O6BBLMT A 603 " occ=0.50
  Time building chain proxies: 7.05, per 1000 atoms: 1.07
  Number of scatterers: 6609
  At special positions: 0
  Unit cell: (69.208, 72.584, 141.792, 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      33     16.00
     O    1239      8.00
     N    1015      7.00
     C    4322      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 206 " - pdb=" SG  CYS A 457 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  86 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 130 " - pdb=" SG  CYS B 186 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  93 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 139 " - pdb=" SG  CYS C 186 " 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: 1.80
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1570

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 9 sheets defined
      45.1% alpha, 18.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.69
  Creating SS restraints...
    Processing helix  chain 'A' and resid 36 through 47
      removed outlier: 3.630A  pdb=" N   GLY A  47 " --> pdb=" O   TYR A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 68
      removed outlier: 4.034A  pdb=" N   GLN A  51 " --> pdb=" O   GLY A  47 " (cutoff:3.500A)
      removed outlier: 5.636A  pdb=" N   GLN A  62 " --> pdb=" O   GLY A  58 " (cutoff:3.500A)
      removed outlier: 5.645A  pdb=" N   ILE A  63 " --> pdb=" O   PHE A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 100
      removed outlier: 3.646A  pdb=" N   ILE A  79 " --> pdb=" O   TYR A  75 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   LEU A  80 " --> pdb=" O   ALA A  76 " (cutoff:3.500A)
      Proline residue:  A  92  - end of helix
    Processing helix  chain 'A' and resid 109 through 128
      Proline residue:  A 118  - end of helix
      removed outlier: 3.521A  pdb=" N   LEU A 122 " --> pdb=" O   PRO A 118 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   TRP A 128 " --> pdb=" O   TYR A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 162
      removed outlier: 3.593A  pdb=" N   TRP A 140 " --> pdb=" O   GLY A 136 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   PHE A 155 " --> pdb=" O   LEU A 151 " (cutoff:3.500A)
      Proline residue:  A 158  - end of helix
    Processing helix  chain 'A' and resid 162 through 167
      removed outlier: 4.456A  pdb=" N   SER A 167 " --> pdb=" O   THR A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 197
      removed outlier: 3.520A  pdb=" N   THR A 192 " --> pdb=" O   THR A 188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 261
      removed outlier: 3.694A  pdb=" N   ALA A 239 " --> pdb=" O   ASP A 235 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 288
    Processing helix  chain 'A' and resid 288 through 311
      removed outlier: 4.062A  pdb=" N   GLY A 310 " --> pdb=" O   MET A 306 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   ASN A 311 " --> pdb=" O   LEU A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 311 through 319
    Processing helix  chain 'A' and resid 325 through 351
      removed outlier: 3.769A  pdb=" N   LEU A 331 " --> pdb=" O   GLN A 327 " (cutoff:3.500A)
      Proline residue:  A 342  - end of helix
    Processing helix  chain 'A' and resid 353 through 363
      removed outlier: 3.694A  pdb=" N   THR A 361 " --> pdb=" O   VAL A 357 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   THR A 362 " --> pdb=" O   TYR A 358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 372
      removed outlier: 4.046A  pdb=" N   VAL A 372 " --> pdb=" O   LEU A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 414
      removed outlier: 3.796A  pdb=" N   TYR A 382 " --> pdb=" O   LEU A 378 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ALA A 393 " --> pdb=" O   GLY A 389 " (cutoff:3.500A)
      Proline residue:  A 399  - end of helix
      Proline residue:  A 404  - end of helix
    Processing helix  chain 'A' and resid 421 through 451
    Processing helix  chain 'A' and resid 460 through 473
    Processing helix  chain 'A' and resid 473 through 488
      removed outlier: 3.658A  pdb=" N   SER A 488 " --> pdb=" O   LEU A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 492 through 495
    Processing helix  chain 'A' and resid 496 through 507
    Processing helix  chain 'B' and resid 117 through 123
    Processing helix  chain 'C' and resid 28 through 31
    Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 5
    Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 12
      removed outlier: 6.446A  pdb=" N   VAL B  32 " --> pdb=" O   TYR B  48 " (cutoff:3.500A)
      removed outlier: 4.714A  pdb=" N   TYR B  48 " --> pdb=" O   VAL B  32 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   TRP B  34 " --> pdb=" O   LEU B  46 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 112 through 114
      removed outlier: 4.993A  pdb=" N   ALA B 127 " --> pdb=" O   ILE B 174 " (cutoff:3.500A)
      removed outlier: 7.206A  pdb=" N   ILE B 174 " --> pdb=" O   ALA B 127 " (cutoff:3.500A)
      removed outlier: 5.682A  pdb=" N   VAL B 129 " --> pdb=" O   LEU B 172 " (cutoff:3.500A)
      removed outlier: 7.295A  pdb=" N   LEU B 172 " --> pdb=" O   VAL B 129 " (cutoff:3.500A)
      removed outlier: 5.492A  pdb=" N   PHE B 131 " --> pdb=" O   ALA B 170 " (cutoff:3.500A)
      removed outlier: 7.140A  pdb=" N   ALA B 170 " --> pdb=" O   PHE B 131 " (cutoff:3.500A)
      removed outlier: 5.299A  pdb=" N   MET B 168 " --> pdb=" O   PRO B 133 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 148 through 149
      removed outlier: 4.842A  pdb=" N   TRP B 143 " --> pdb=" O   GLN B 149 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 3 through 6
      removed outlier: 3.531A  pdb=" N   ALA C  18 " --> pdb=" O   ILE C  81 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   ASN C  76 " --> pdb=" O   SER C  71 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 56 through 58
      removed outlier: 5.158A  pdb=" N   TRP C  46 " --> pdb=" O   PHE C  38 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   PHE C  38 " --> pdb=" O   TRP C  46 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   ALA C  48 " --> pdb=" O   TRP C  36 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 121 through 123
      removed outlier: 6.042A  pdb=" N   TRP C 170 " --> pdb=" O   GLY C 143 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 121 through 123
      removed outlier: 6.042A  pdb=" N   TRP C 170 " --> pdb=" O   GLY C 143 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   LEU C 169 " --> pdb=" O   ASN C 166 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 149 through 151

    376 hydrogen bonds defined for protein.
    1064 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: 1.99

  Time building geometry restraints manager: 2.08 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1947
        1.34 -     1.46: 1719
        1.46 -     1.58: 3055
        1.58 -     1.70: 22
        1.70 -     1.81: 46
  Bond restraints: 6789
  Sorted by residual:
  bond pdb=" C1B LMT A 601 "
       pdb=" O5B LMT A 601 "
    ideal  model  delta    sigma   weight residual
    1.393  1.515 -0.122 2.00e-02 2.50e+03 3.70e+01
  bond pdb=" C1B LMT A 602 "
       pdb=" O5B LMT A 602 "
    ideal  model  delta    sigma   weight residual
    1.393  1.514 -0.121 2.00e-02 2.50e+03 3.67e+01
  bond pdb=" C1B LMT A 609 "
       pdb=" O5B LMT A 609 "
    ideal  model  delta    sigma   weight residual
    1.393  1.513 -0.120 2.00e-02 2.50e+03 3.62e+01
  bond pdb=" C1BALMT A 603 "
       pdb=" O5BALMT A 603 "
    ideal  model  delta    sigma   weight residual
    1.393  1.513 -0.120 2.00e-02 2.50e+03 3.60e+01
  bond pdb=" C1BBLMT A 603 "
       pdb=" O5BBLMT A 603 "
    ideal  model  delta    sigma   weight residual
    1.393  1.512 -0.119 2.00e-02 2.50e+03 3.55e+01
  ... (remaining 6784 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.91: 8772
        1.91 -     3.81: 311
        3.81 -     5.72: 99
        5.72 -     7.62: 78
        7.62 -     9.53: 14
  Bond angle restraints: 9274
  Sorted by residual:
  angle pdb=" C   THR A  90 "
        pdb=" N   ASP A  91 "
        pdb=" CA  ASP A  91 "
      ideal   model   delta    sigma   weight residual
     121.80  112.97    8.83 2.44e+00 1.68e-01 1.31e+01
  angle pdb=" N   GLY B  97 "
        pdb=" CA  GLY B  97 "
        pdb=" C   GLY B  97 "
      ideal   model   delta    sigma   weight residual
     113.18  121.74   -8.56 2.37e+00 1.78e-01 1.30e+01
  angle pdb=" N   TRP C  95 "
        pdb=" CA  TRP C  95 "
        pdb=" C   TRP C  95 "
      ideal   model   delta    sigma   weight residual
     109.24  103.88    5.36 1.67e+00 3.59e-01 1.03e+01
  angle pdb=" C1B LMT A 606 "
        pdb=" O1B LMT A 606 "
        pdb=" C4' LMT A 606 "
      ideal   model   delta    sigma   weight residual
     117.87  108.34    9.53 3.00e+00 1.11e-01 1.01e+01
  angle pdb=" N   ASP A 235 "
        pdb=" CA  ASP A 235 "
        pdb=" C   ASP A 235 "
      ideal   model   delta    sigma   weight residual
     112.89  108.96    3.93 1.24e+00 6.50e-01 1.00e+01
  ... (remaining 9269 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.38: 3866
       23.38 -    46.76: 229
       46.76 -    70.14: 86
       70.14 -    93.52: 52
       93.52 -   116.90: 96
  Dihedral angle restraints: 4329
    sinusoidal: 1865
      harmonic: 2464
  Sorted by residual:
  dihedral pdb=" CA  ARG A 455 "
           pdb=" C   ARG A 455 "
           pdb=" N   GLY A 456 "
           pdb=" CA  GLY A 456 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.99   24.01     0      5.00e+00 4.00e-02 2.31e+01
  dihedral pdb=" C1B LMT A 602 "
           pdb=" C2B LMT A 602 "
           pdb=" C3B LMT A 602 "
           pdb=" O3B LMT A 602 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -175.52  -58.62 -116.90     1      3.00e+01 1.11e-03 1.55e+01
  dihedral pdb=" O2B LMT A 606 "
           pdb=" C2B LMT A 606 "
           pdb=" C3B LMT A 606 "
           pdb=" O3B LMT A 606 "
      ideal   model   delta sinusoidal    sigma   weight residual
      63.73 -179.47 -116.80     1      3.00e+01 1.11e-03 1.55e+01
  ... (remaining 4326 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 825
       0.050 -    0.100: 219
       0.100 -    0.150: 56
       0.150 -    0.200: 10
       0.200 -    0.250: 2
  Chirality restraints: 1112
  Sorted by residual:
  chirality pdb=" C1B LMT B 301 "
            pdb=" C2B LMT B 301 "
            pdb=" O1B LMT B 301 "
            pdb=" O5B LMT B 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.20   -2.45    0.25 2.00e-01 2.50e+01 1.56e+00
  chirality pdb=" C4' LMT B 301 "
            pdb=" C3' LMT B 301 "
            pdb=" C5' LMT B 301 "
            pdb=" O1B LMT B 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.55   -2.35   -0.21 2.00e-01 2.50e+01 1.06e+00
  chirality pdb=" C1B LMT A 608 "
            pdb=" C2B LMT A 608 "
            pdb=" O1B LMT A 608 "
            pdb=" O5B LMT A 608 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.20   -2.40    0.19 2.00e-01 2.50e+01 9.48e-01
  ... (remaining 1109 not shown)

  Planarity restraints: 1119
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 251 "    0.011 2.00e-02 2.50e+03   2.29e-02 5.23e+00
        pdb=" C   TYR A 251 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   TYR A 251 "    0.015 2.00e-02 2.50e+03
        pdb=" N   VAL A 252 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE C 103 "   -0.036 5.00e-02 4.00e+02   5.49e-02 4.83e+00
        pdb=" N   PRO C 104 "    0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO C 104 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO C 104 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP C  46 "    0.036 5.00e-02 4.00e+02   5.48e-02 4.81e+00
        pdb=" N   PRO C  47 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO C  47 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO C  47 "    0.030 5.00e-02 4.00e+02
  ... (remaining 1116 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1503
        2.79 -     3.31: 6082
        3.31 -     3.84: 11173
        3.84 -     4.37: 12312
        4.37 -     4.90: 22184
  Nonbonded interactions: 53254
  Sorted by model distance:
  nonbonded pdb=" O   TRP A  86 "
            pdb=" OG1 THR A  90 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" O   TYR A 452 "
            pdb=" ND2 ASN C  99 "
     model   vdw
     2.275 3.120
  nonbonded pdb=" OD1 ASP A  67 "
            pdb=" OH  TYR A 452 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" O   GLN A 135 "
            pdb=" O6' LMT A 608 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" NZ  LYS B  11 "
            pdb=" O   ARG B  19 "
     model   vdw
     2.304 3.120
  ... (remaining 53249 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=0.50 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.930
  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:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     21.950
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
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      :  0.011   0.122   6789  Z= 0.729
  Angle     :  1.101   9.528   9274  Z= 0.457
  Chirality :  0.050   0.250   1112
  Planarity :  0.006   0.055   1119
  Dihedral  : 27.925 116.897   2744
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.89 %
    Favored  : 93.11 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  :  8.22 %
    Favored  : 91.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.99 (0.28), residues: 865
  helix:  0.61 (0.26), residues: 376
  sheet: -0.59 (0.40), residues: 180
  loop : -2.26 (0.34), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C  33 
 HIS   0.004   0.002   HIS A 156 
 PHE   0.029   0.002   PHE C  38 
 TYR   0.008   0.001   TYR A 251 
 ARG   0.002   0.000   ARG C  31 

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 149
  time to evaluate  : 0.627 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 PHE cc_start: 0.7700 (m-80) cc_final: 0.7475 (m-10)
REVERT: A  109 MET cc_start: 0.8205 (mmt) cc_final: 0.7884 (mmt)
REVERT: A  181 MET cc_start: 0.7940 (mtt) cc_final: 0.7675 (mtp)
REVERT: A  189 LEU cc_start: 0.8416 (tp) cc_final: 0.8213 (tt)
REVERT: A  427 PHE cc_start: 0.8184 (t80) cc_final: 0.7954 (t80)
REVERT: B   60 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.6816 (mt0)
  outliers start: 3
  outliers final: 0
  residues processed: 151
  average time/residue: 0.1898
  time to fit residues: 37.5198
Evaluate side-chains
  123 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 122
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   60 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    0.9980
   chunk 65 optimal weight:    8.9990
   chunk 36 optimal weight:    6.9990
   chunk 22 optimal weight:   40.0000
   chunk 43 optimal weight:    0.6980
   chunk 34 optimal weight:    0.7980
   chunk 67 optimal weight:    3.9990
   chunk 26 optimal weight:    0.5980
   chunk 40 optimal weight:    0.9980
   chunk 50 optimal weight:    0.7980
   chunk 78 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 149 GLN
A 195 GLN
B  36 ASN
B  37 GLN
C  50 ASN
C  57 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.164354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.144910 restraints weight = 30821.028|
|-----------------------------------------------------------------------------|
r_work (start): 0.3703 rms_B_bonded: 3.12
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3703
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3703 r_free = 0.3703    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3701 r_free = 0.3701    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3701
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.1685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   6789  Z= 0.308
  Angle     :  0.871  11.607   9274  Z= 0.384
  Chirality :  0.051   0.297   1112
  Planarity :  0.005   0.055   1119
  Dihedral  : 20.430  82.010   1587
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 11.13 %
    Favored  : 86.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.48 (0.29), residues: 865
  helix:  1.33 (0.27), residues: 376
  sheet: -0.54 (0.40), residues: 179
  loop : -2.29 (0.33), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP A 344 
 HIS   0.002   0.001   HIS A 156 
 PHE   0.025   0.002   PHE C  38 
 TYR   0.011   0.001   TYR A 159 
 ARG   0.005   0.001   ARG A  84 

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 124
  time to evaluate  : 0.662 
Fit side-chains
   revert: symmetry clash
REVERT: A  181 MET cc_start: 0.8052 (mtt) cc_final: 0.7772 (mtp)
REVERT: A  206 CYS cc_start: 0.5253 (m) cc_final: 0.4845 (m)
REVERT: A  291 TYR cc_start: 0.7674 (OUTLIER) cc_final: 0.5844 (t80)
REVERT: B   60 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.7069 (mt0)
REVERT: B  198 MET cc_start: 0.7248 (mmm) cc_final: 0.6768 (mmt)
REVERT: C   25 LYS cc_start: 0.7551 (mmtt) cc_final: 0.7332 (mmtt)
  outliers start: 15
  outliers final: 6
  residues processed: 133
  average time/residue: 0.1989
  time to fit residues: 35.2260
Evaluate side-chains
  118 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 110
  time to evaluate  : 0.615 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  431 PHE
Chi-restraints excluded: chain B residue    4 ILE
Chi-restraints excluded: chain B residue   60 GLN
Chi-restraints excluded: chain B residue  174 ILE
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  151 THR
Chi-restraints excluded: chain C residue  163 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 72 optimal weight:    0.9980
   chunk 25 optimal weight:    0.3980
   chunk 38 optimal weight:    0.7980
   chunk 56 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9980
   chunk 55 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9980
   chunk 83 optimal weight:    0.9990
   chunk 42 optimal weight:    0.8980
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 238 ASN
C  50 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.164702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.145276 restraints weight = 30865.109|
|-----------------------------------------------------------------------------|
r_work (start): 0.3707 rms_B_bonded: 3.00
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3707
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3707 r_free = 0.3707    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3707 r_free = 0.3707    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3707
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7614
moved from start:          0.2142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   6789  Z= 0.274
  Angle     :  0.796  11.723   9274  Z= 0.360
  Chirality :  0.048   0.335   1112
  Planarity :  0.005   0.054   1119
  Dihedral  : 14.734  66.739   1587
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.19 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 13.53 %
    Favored  : 84.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.29), residues: 865
  helix:  1.47 (0.27), residues: 376
  sheet: -0.65 (0.39), residues: 181
  loop : -2.28 (0.34), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 344 
 HIS   0.003   0.002   HIS A 156 
 PHE   0.025   0.002   PHE C  38 
 TYR   0.009   0.001   TYR A 251 
 ARG   0.006   0.001   ARG B 191 

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 115
  time to evaluate  : 0.627 
Fit side-chains
   revert: symmetry clash
REVERT: A  181 MET cc_start: 0.8069 (mtt) cc_final: 0.7833 (mtp)
REVERT: A  291 TYR cc_start: 0.7772 (OUTLIER) cc_final: 0.6075 (t80)
REVERT: B   60 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.7155 (mt0)
  outliers start: 11
  outliers final: 6
  residues processed: 121
  average time/residue: 0.2043
  time to fit residues: 32.3205
Evaluate side-chains
  119 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 111
  time to evaluate  : 0.624 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 ASP
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  431 PHE
Chi-restraints excluded: chain B residue    4 ILE
Chi-restraints excluded: chain B residue   60 GLN
Chi-restraints excluded: chain B residue  174 ILE
Chi-restraints excluded: chain C residue   50 ASN
Chi-restraints excluded: chain C residue  163 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 67 optimal weight:    3.9990
   chunk 72 optimal weight:    0.0060
   chunk 5 optimal weight:    0.7980
   chunk 22 optimal weight:    0.0980
   chunk 24 optimal weight:    0.7980
   chunk 42 optimal weight:    0.5980
   chunk 73 optimal weight:    0.8980
   chunk 38 optimal weight:    0.5980
   chunk 69 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0870
   overall best weight:    0.2774

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

Flipped N/Q/H residues before XYZ refinement:
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  50 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.166647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.144061 restraints weight = 31218.340|
|-----------------------------------------------------------------------------|
r_work (start): 0.3713 rms_B_bonded: 3.84
r_work (final): 0.3713
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3708
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3708 r_free = 0.3708    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3708 r_free = 0.3708    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3708
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.2438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6789  Z= 0.188
  Angle     :  0.721  10.747   9274  Z= 0.328
  Chirality :  0.045   0.318   1112
  Planarity :  0.005   0.051   1119
  Dihedral  : 12.948  59.915   1587
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 14.21 %
    Favored  : 83.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.30), residues: 865
  helix:  1.81 (0.27), residues: 375
  sheet: -0.55 (0.38), residues: 183
  loop : -2.22 (0.34), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 344 
 HIS   0.001   0.001   HIS A 156 
 PHE   0.020   0.002   PHE A 427 
 TYR   0.008   0.001   TYR A 251 
 ARG   0.006   0.001   ARG B 191 

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 120
  time to evaluate  : 0.652 
Fit side-chains
   revert: symmetry clash
REVERT: A  181 MET cc_start: 0.7945 (mtt) cc_final: 0.7617 (mtp)
REVERT: A  291 TYR cc_start: 0.7729 (OUTLIER) cc_final: 0.5422 (t80)
REVERT: B   60 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.7118 (mt0)
REVERT: B  198 MET cc_start: 0.7563 (mmm) cc_final: 0.7187 (mmt)
  outliers start: 11
  outliers final: 8
  residues processed: 126
  average time/residue: 0.1953
  time to fit residues: 32.4393
Evaluate side-chains
  128 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 118
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 ASP
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  431 PHE
Chi-restraints excluded: chain B residue    4 ILE
Chi-restraints excluded: chain B residue   60 GLN
Chi-restraints excluded: chain B residue   63 GLN
Chi-restraints excluded: chain B residue  174 ILE
Chi-restraints excluded: chain C residue   50 ASN
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  151 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 68 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   chunk 13 optimal weight:    0.6980
   chunk 75 optimal weight:    0.0070
   chunk 28 optimal weight:    0.5980
   chunk 60 optimal weight:    0.8980
   chunk 5 optimal weight:    0.6980
   chunk 8 optimal weight:    0.6980
   chunk 49 optimal weight:    0.7980
   chunk 83 optimal weight:    0.8980
   overall best weight:    0.5198

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

Flipped N/Q/H residues before XYZ refinement:
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  50 ASN
** C 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.165273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.143141 restraints weight = 30393.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.3699 rms_B_bonded: 3.71
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3699
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3699 r_free = 0.3699    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3699 r_free = 0.3699    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3699
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.2527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6789  Z= 0.234
  Angle     :  0.725   9.965   9274  Z= 0.336
  Chirality :  0.045   0.275   1112
  Planarity :  0.005   0.053   1119
  Dihedral  : 12.017  59.806   1587
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 14.04 %
    Favored  : 82.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.29), residues: 865
  helix:  1.83 (0.27), residues: 376
  sheet: -0.59 (0.38), residues: 189
  loop : -2.24 (0.34), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 344 
 HIS   0.002   0.001   HIS A 156 
 PHE   0.023   0.002   PHE C  38 
 TYR   0.009   0.001   TYR A 251 
 ARG   0.006   0.001   ARG B 191 

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 118
  time to evaluate  : 0.717 
Fit side-chains
REVERT: A  164 MET cc_start: 0.7697 (mmm) cc_final: 0.7353 (mmm)
REVERT: A  173 ARG cc_start: 0.7704 (mtt-85) cc_final: 0.7446 (mtt90)
REVERT: A  181 MET cc_start: 0.7920 (mtt) cc_final: 0.7597 (mtp)
REVERT: A  291 TYR cc_start: 0.7767 (OUTLIER) cc_final: 0.5373 (t80)
REVERT: B   60 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7070 (mt0)
REVERT: B  198 MET cc_start: 0.7749 (mmm) cc_final: 0.7452 (mmt)
  outliers start: 18
  outliers final: 12
  residues processed: 125
  average time/residue: 0.1951
  time to fit residues: 32.3048
Evaluate side-chains
  128 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 114
  time to evaluate  : 0.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 ASP
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  431 PHE
Chi-restraints excluded: chain B residue    4 ILE
Chi-restraints excluded: chain B residue   60 GLN
Chi-restraints excluded: chain B residue   63 GLN
Chi-restraints excluded: chain B residue  139 ILE
Chi-restraints excluded: chain B residue  168 MET
Chi-restraints excluded: chain B residue  174 ILE
Chi-restraints excluded: chain C residue   50 ASN
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  151 THR
Chi-restraints excluded: chain C residue  176 VAL
Chi-restraints excluded: chain C residue  188 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 82 optimal weight:    0.3980
   chunk 56 optimal weight:    0.0270
   chunk 10 optimal weight:    0.5980
   chunk 59 optimal weight:    0.4980
   chunk 19 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 9 optimal weight:    0.8980
   chunk 23 optimal weight:   30.0000
   chunk 34 optimal weight:    0.5980
   chunk 39 optimal weight:    2.9990
   overall best weight:    0.4238

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

Flipped N/Q/H residues before XYZ refinement:
C  50 ASN
C 112 ASN
** C 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.165844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.142703 restraints weight = 33642.230|
|-----------------------------------------------------------------------------|
r_work (start): 0.3696 rms_B_bonded: 4.12
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3693
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3693 r_free = 0.3693    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3693 r_free = 0.3693    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3693
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.2631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6789  Z= 0.212
  Angle     :  0.697  10.107   9274  Z= 0.324
  Chirality :  0.044   0.256   1112
  Planarity :  0.005   0.053   1119
  Dihedral  : 11.320  59.715   1587
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 14.55 %
    Favored  : 82.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.30), residues: 865
  helix:  1.92 (0.27), residues: 376
  sheet: -0.44 (0.38), residues: 189
  loop : -2.26 (0.34), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.002   TRP A 344 
 HIS   0.002   0.001   HIS A 156 
 PHE   0.022   0.002   PHE C  38 
 TYR   0.008   0.001   TYR A 251 
 ARG   0.007   0.001   ARG B 191 

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 121
  time to evaluate  : 0.648 
Fit side-chains
REVERT: A  164 MET cc_start: 0.7685 (mmm) cc_final: 0.7356 (mmm)
REVERT: A  173 ARG cc_start: 0.7684 (mtt-85) cc_final: 0.7440 (mtt90)
REVERT: A  181 MET cc_start: 0.7940 (mtt) cc_final: 0.7626 (mtp)
REVERT: A  291 TYR cc_start: 0.7711 (OUTLIER) cc_final: 0.5215 (t80)
REVERT: A  318 TYR cc_start: 0.8583 (m-80) cc_final: 0.8200 (m-80)
REVERT: B   60 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.7219 (mt0)
REVERT: B  198 MET cc_start: 0.7756 (mmm) cc_final: 0.7496 (mmt)
  outliers start: 20
  outliers final: 10
  residues processed: 128
  average time/residue: 0.1823
  time to fit residues: 31.0573
Evaluate side-chains
  127 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 115
  time to evaluate  : 0.632 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 ASP
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  431 PHE
Chi-restraints excluded: chain B residue    4 ILE
Chi-restraints excluded: chain B residue   60 GLN
Chi-restraints excluded: chain B residue   63 GLN
Chi-restraints excluded: chain B residue  139 ILE
Chi-restraints excluded: chain B residue  174 ILE
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  151 THR
Chi-restraints excluded: chain C residue  176 VAL
Chi-restraints excluded: chain C residue  188 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 58 optimal weight:    4.9990
   chunk 29 optimal weight:    0.0980
   chunk 35 optimal weight:    0.6980
   chunk 6 optimal weight:    0.6980
   chunk 46 optimal weight:    2.9990
   chunk 61 optimal weight:    0.5980
   chunk 66 optimal weight:    0.0570
   chunk 44 optimal weight:    3.9990
   overall best weight:    0.4298

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

Flipped N/Q/H residues before XYZ refinement:
C 112 ASN
** C 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.166225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.143668 restraints weight = 32935.544|
|-----------------------------------------------------------------------------|
r_work (start): 0.3707 rms_B_bonded: 3.88
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3706
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3706 r_free = 0.3706    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3706 r_free = 0.3706    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3706
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.2822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6789  Z= 0.209
  Angle     :  0.674   9.352   9274  Z= 0.320
  Chirality :  0.042   0.188   1112
  Planarity :  0.005   0.053   1119
  Dihedral  : 10.416  59.250   1587
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 15.24 %
    Favored  : 81.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.30), residues: 865
  helix:  1.99 (0.27), residues: 376
  sheet: -0.41 (0.39), residues: 182
  loop : -2.20 (0.33), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.002   TRP A 344 
 HIS   0.002   0.001   HIS A 156 
 PHE   0.025   0.002   PHE A 427 
 TYR   0.008   0.001   TYR A 251 
 ARG   0.007   0.001   ARG B 191 

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 121
  time to evaluate  : 0.808 
Fit side-chains
REVERT: A  164 MET cc_start: 0.7696 (mmm) cc_final: 0.7381 (mmm)
REVERT: A  173 ARG cc_start: 0.7743 (mtt-85) cc_final: 0.7510 (mtt90)
REVERT: A  181 MET cc_start: 0.7911 (mtt) cc_final: 0.7609 (mtp)
REVERT: A  318 TYR cc_start: 0.8626 (m-80) cc_final: 0.8240 (m-80)
REVERT: B   60 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7288 (mt0)
REVERT: B  198 MET cc_start: 0.7787 (mmm) cc_final: 0.7562 (mmt)
  outliers start: 17
  outliers final: 10
  residues processed: 124
  average time/residue: 0.2054
  time to fit residues: 34.4334
Evaluate side-chains
  126 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 115
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 ASP
Chi-restraints excluded: chain A residue  431 PHE
Chi-restraints excluded: chain A residue  458 THR
Chi-restraints excluded: chain B residue    4 ILE
Chi-restraints excluded: chain B residue   60 GLN
Chi-restraints excluded: chain B residue   63 GLN
Chi-restraints excluded: chain B residue  174 ILE
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  151 THR
Chi-restraints excluded: chain C residue  163 SER
Chi-restraints excluded: chain C residue  176 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 74 optimal weight:    0.0980
   chunk 20 optimal weight:    0.5980
   chunk 79 optimal weight:    0.4980
   chunk 68 optimal weight:    0.6980
   chunk 73 optimal weight:    0.7980
   chunk 39 optimal weight:    2.9990
   chunk 9 optimal weight:    0.4980
   chunk 15 optimal weight:    0.9980
   chunk 46 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0870
   chunk 42 optimal weight:    0.6980
   overall best weight:    0.3558

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

Flipped N/Q/H residues before XYZ refinement:
A 328 ASN
C  50 ASN
C 112 ASN
C 166 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.166557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.144164 restraints weight = 27958.108|
|-----------------------------------------------------------------------------|
r_work (start): 0.3714 rms_B_bonded: 3.64
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3715
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3715 r_free = 0.3715    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3715 r_free = 0.3715    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3715
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.2976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6789  Z= 0.203
  Angle     :  0.664   9.277   9274  Z= 0.317
  Chirality :  0.042   0.176   1112
  Planarity :  0.005   0.052   1119
  Dihedral  :  9.995  59.670   1587
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 16.27 %
    Favored  : 80.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.30), residues: 865
  helix:  1.97 (0.27), residues: 377
  sheet: -0.39 (0.39), residues: 182
  loop : -2.16 (0.33), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP A 344 
 HIS   0.002   0.001   HIS A 156 
 PHE   0.024   0.002   PHE A 427 
 TYR   0.008   0.001   TYR A 251 
 ARG   0.006   0.001   ARG B 191 

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 0.655 
Fit side-chains
REVERT: A  181 MET cc_start: 0.7818 (mtt) cc_final: 0.7552 (mtp)
REVERT: A  291 TYR cc_start: 0.7820 (OUTLIER) cc_final: 0.5259 (t80)
REVERT: A  318 TYR cc_start: 0.8648 (m-80) cc_final: 0.8268 (m-80)
REVERT: B   60 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.7590 (mt0)
REVERT: B  198 MET cc_start: 0.7823 (mmm) cc_final: 0.7595 (mmt)
  outliers start: 17
  outliers final: 11
  residues processed: 121
  average time/residue: 0.1845
  time to fit residues: 29.6784
Evaluate side-chains
  122 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 109
  time to evaluate  : 0.675 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 ASP
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  431 PHE
Chi-restraints excluded: chain A residue  458 THR
Chi-restraints excluded: chain B residue    4 ILE
Chi-restraints excluded: chain B residue   60 GLN
Chi-restraints excluded: chain B residue   63 GLN
Chi-restraints excluded: chain B residue  174 ILE
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  151 THR
Chi-restraints excluded: chain C residue  163 SER
Chi-restraints excluded: chain C residue  190 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 9 optimal weight:    0.0980
   chunk 73 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 47 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 49 optimal weight:    0.8980
   chunk 32 optimal weight:    0.6980
   chunk 79 optimal weight:    0.3980
   chunk 3 optimal weight:    0.1980
   overall best weight:    0.4180

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

Flipped N/Q/H residues before XYZ refinement:
C 112 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.165892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.146002 restraints weight = 24134.627|
|-----------------------------------------------------------------------------|
r_work (start): 0.3738 rms_B_bonded: 2.92
r_work: 0.3237 rms_B_bonded: 4.49 restraints_weight: 0.5000
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3215
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3215 r_free = 0.3215    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3214 r_free = 0.3214    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3214
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.3058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6789  Z= 0.209
  Angle     :  0.675  10.615   9274  Z= 0.319
  Chirality :  0.042   0.177   1112
  Planarity :  0.005   0.051   1119
  Dihedral  :  9.714  59.748   1587
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 17.64 %
    Favored  : 79.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.29), residues: 865
  helix:  2.00 (0.27), residues: 376
  sheet: -0.40 (0.39), residues: 182
  loop : -2.22 (0.33), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A 344 
 HIS   0.002   0.001   HIS A 156 
 PHE   0.025   0.002   PHE A 427 
 TYR   0.008   0.001   TYR A 251 
 ARG   0.006   0.001   ARG B 191 

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 109
  time to evaluate  : 0.598 
Fit side-chains
REVERT: A  181 MET cc_start: 0.7835 (mtt) cc_final: 0.7587 (mtp)
REVERT: A  291 TYR cc_start: 0.7521 (OUTLIER) cc_final: 0.5110 (t80)
REVERT: A  318 TYR cc_start: 0.8888 (m-80) cc_final: 0.8468 (m-80)
REVERT: A  424 PHE cc_start: 0.8531 (t80) cc_final: 0.7910 (t80)
REVERT: B   60 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.7884 (mt0)
REVERT: B  198 MET cc_start: 0.8466 (mmm) cc_final: 0.8107 (mmt)
  outliers start: 15
  outliers final: 11
  residues processed: 114
  average time/residue: 0.1880
  time to fit residues: 28.4688
Evaluate side-chains
  121 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 0.659 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 ASP
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  431 PHE
Chi-restraints excluded: chain A residue  458 THR
Chi-restraints excluded: chain B residue    4 ILE
Chi-restraints excluded: chain B residue   60 GLN
Chi-restraints excluded: chain B residue   63 GLN
Chi-restraints excluded: chain B residue  174 ILE
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  163 SER
Chi-restraints excluded: chain C residue  176 VAL
Chi-restraints excluded: chain C residue  190 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 38 optimal weight:    0.7980
   chunk 72 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   chunk 30 optimal weight:    0.0670
   chunk 50 optimal weight:    0.9980
   chunk 35 optimal weight:    0.0050
   chunk 62 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 31 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9990
   overall best weight:    0.4332

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

Flipped N/Q/H residues before XYZ refinement:
C 112 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.166852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.143259 restraints weight = 36991.287|
|-----------------------------------------------------------------------------|
r_work (start): 0.3694 rms_B_bonded: 4.41
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3690
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3690 r_free = 0.3690    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3690 r_free = 0.3690    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3690
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.3126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6789  Z= 0.211
  Angle     :  0.670  10.593   9274  Z= 0.318
  Chirality :  0.042   0.177   1112
  Planarity :  0.005   0.051   1119
  Dihedral  :  9.433  59.910   1587
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 18.15 %
    Favored  : 79.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.29), residues: 865
  helix:  1.98 (0.27), residues: 377
  sheet: -0.51 (0.41), residues: 167
  loop : -2.22 (0.32), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A 344 
 HIS   0.002   0.001   HIS A 156 
 PHE   0.025   0.002   PHE A 427 
 TYR   0.009   0.001   TYR A 358 
 ARG   0.007   0.001   ARG B 191 

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 0.669 
Fit side-chains
REVERT: A  181 MET cc_start: 0.7894 (mtt) cc_final: 0.7643 (mtp)
REVERT: A  291 TYR cc_start: 0.7943 (OUTLIER) cc_final: 0.5812 (t80)
REVERT: A  318 TYR cc_start: 0.8607 (m-80) cc_final: 0.8210 (m-80)
REVERT: A  424 PHE cc_start: 0.7873 (t80) cc_final: 0.7355 (t80)
  outliers start: 12
  outliers final: 11
  residues processed: 113
  average time/residue: 0.1994
  time to fit residues: 29.8673
Evaluate side-chains
  121 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 0.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 ASP
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  431 PHE
Chi-restraints excluded: chain B residue    4 ILE
Chi-restraints excluded: chain B residue   63 GLN
Chi-restraints excluded: chain B residue  174 ILE
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain C residue  112 ASN
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  163 SER
Chi-restraints excluded: chain C residue  176 VAL
Chi-restraints excluded: chain C residue  190 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 52 optimal weight:    0.5980
   chunk 11 optimal weight:    0.5980
   chunk 4 optimal weight:    0.5980
   chunk 61 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 71 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
C 112 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.164239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.141960 restraints weight = 28624.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.3694 rms_B_bonded: 3.62
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3688
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3688 r_free = 0.3688    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3688 r_free = 0.3688    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3688
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.3102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   6789  Z= 0.273
  Angle     :  0.698  10.183   9274  Z= 0.334
  Chirality :  0.043   0.180   1112
  Planarity :  0.005   0.050   1119
  Dihedral  :  9.384  59.835   1584
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.66 %
    Favored  : 93.34 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 18.15 %
    Favored  : 79.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.05 (0.29), residues: 865
  helix:  1.87 (0.27), residues: 377
  sheet: -0.48 (0.39), residues: 185
  loop : -2.27 (0.33), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A 344 
 HIS   0.003   0.001   HIS A 156 
 PHE   0.025   0.002   PHE C  38 
 TYR   0.010   0.001   TYR B 136 
 ARG   0.007   0.001   ARG B 191 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2848.85 seconds
wall clock time: 51 minutes 52.93 seconds (3112.93 seconds total)