Starting phenix.real_space_refine
on Wed Feb 12 12:22:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d2v_27151/02_2025/8d2v_27151.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d2v_27151/02_2025/8d2v_27151.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8d2v_27151/02_2025/8d2v_27151.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d2v_27151/02_2025/8d2v_27151.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d2v_27151/02_2025/8d2v_27151.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d2v_27151/02_2025/8d2v_27151.cif"
  }
  resolution = 4.1
  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=   0.035
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 1603 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: 6
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      30      5.16       5
     Na      1      4.78       5
     C    4186      2.51       5
     N     995      2.21       5
     O    1175      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6388
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3326
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 460, 3304
          Classifications: {'peptide': 460}
          Incomplete info: {'truncation_to_alanine': 88}
          Link IDs: {'PTRANS': 20, 'TRANS': 439}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 299
          Unresolved non-hydrogen angles: 362
          Unresolved non-hydrogen dihedrals: 245
          Unresolved non-hydrogen chiralities: 20
          Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 9}
          Unresolved non-hydrogen planarities: 157
      Conformer: "B"
        Number of residues, atoms: 460, 3304
          Classifications: {'peptide': 460}
          Incomplete info: {'truncation_to_alanine': 88}
          Link IDs: {'PTRANS': 20, 'TRANS': 439}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 299
          Unresolved non-hydrogen angles: 362
          Unresolved non-hydrogen dihedrals: 245
          Unresolved non-hydrogen chiralities: 20
          Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 9}
          Unresolved non-hydrogen planarities: 157
          bond proxies already assigned to first conformer: 3368
    Chain: "B"
      Number of atoms: 1375
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1375
          Classifications: {'peptide': 201}
          Incomplete info: {'truncation_to_alanine': 27}
          Link IDs: {'PTRANS': 14, 'TRANS': 186}
          Unresolved non-hydrogen bonds: 78
          Unresolved non-hydrogen angles: 95
          Unresolved non-hydrogen dihedrals: 61
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 44
    Chain: "C"
      Number of atoms: 1371
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 203, 1371
          Classifications: {'peptide': 203}
          Incomplete info: {'truncation_to_alanine': 28}
          Link IDs: {'PTRANS': 12, 'TRANS': 190}
          Unresolved non-hydrogen bonds: 82
          Unresolved non-hydrogen angles: 97
          Unresolved non-hydrogen dihedrals: 67
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 34
    Chain: "A"
      Number of atoms: 316
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 316
          Unusual residues: {' NA': 1, 'LMT': 8, 'ZGS': 1}
          Classifications: {'undetermined': 10}
          Link IDs: {None: 9}
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N  AARG A  84 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A  84 " occ=0.50
    residue:
      pdb=" N  APHE A 396 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE A 396 " occ=0.50
  Time building chain proxies: 6.63, per 1000 atoms: 1.04
  Number of scatterers: 6388
  At special positions: 0
  Unit cell: (71.74, 72.584, 141.792, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      30     16.00
     P       1     15.00
     Na      1     11.00
     O    1175      8.00
     N     995      7.00
     C    4186      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    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: 1.56
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1568

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 9 sheets defined
      45.5% alpha, 18.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.55
  Creating SS restraints...
    Processing helix  chain 'A' and resid 36 through 48
    Processing helix  chain 'A' and resid 48 through 68
      removed outlier: 3.783A  pdb=" N   GLY A  58 " --> pdb=" O   GLY A  54 " (cutoff:3.500A)
      removed outlier: 6.030A  pdb=" N   GLN A  62 " --> pdb=" O   GLY A  58 " (cutoff:3.500A)
      removed outlier: 5.328A  pdb=" N   ILE A  63 " --> pdb=" O   PHE A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 100
      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: 3.590A  pdb=" N   LEU A 122 " --> pdb=" O   PRO A 118 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   PHE A 125 " --> pdb=" O   VAL A 121 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   TRP A 128 " --> pdb=" O   TYR A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 162
      Proline residue:  A 158  - end of helix
    Processing helix  chain 'A' and resid 162 through 167
      removed outlier: 4.595A  pdb=" N   SER A 167 " --> pdb=" O   THR A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 200
    Processing helix  chain 'A' and resid 232 through 262
    Processing helix  chain 'A' and resid 277 through 288
    Processing helix  chain 'A' and resid 288 through 320
      removed outlier: 3.579A  pdb=" N   LEU A 308 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
      removed outlier: 4.519A  pdb=" N   GLU A 309 " --> pdb=" O   PHE A 305 " (cutoff:3.500A)
      removed outlier: 4.362A  pdb=" N   GLY A 310 " --> pdb=" O   MET A 306 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   ASN A 311 " --> pdb=" O   LEU A 307 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   LEU A 314 " --> pdb=" O   GLY A 310 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   LEU A 320 " --> pdb=" O   CYS A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 351
      Proline residue:  A 342  - end of helix
    Processing helix  chain 'A' and resid 352 through 362
      removed outlier: 3.635A  pdb=" N   THR A 361 " --> pdb=" O   VAL A 357 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   THR A 362 " --> pdb=" O   TYR A 358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 372
      removed outlier: 4.523A  pdb=" N   PHE A 367 " --> pdb=" O   SER A 363 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   VAL A 372 " --> pdb=" O   LEU A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 377 through 414
      Proline residue:  A 399  - end of helix
      Proline residue:  A 404  - end of helix
    Processing helix  chain 'A' and resid 419 through 451
      removed outlier: 3.522A  pdb=" N   PHE A 424 " --> pdb=" O   HIS A 420 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   SER A 426 " --> pdb=" O   ALA A 422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 471
    Processing helix  chain 'A' and resid 473 through 488
    Processing helix  chain 'A' and resid 493 through 507
      removed outlier: 3.865A  pdb=" N   GLN A 497 " --> pdb=" O   GLU A 493 " (cutoff:3.500A)
      removed outlier: 5.177A  pdb=" N   ASN A 499 " --> pdb=" O   LYS A 495 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 123
    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: 6.005A  pdb=" N   LYS B  11 " --> pdb=" O   ASN B 102 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   VAL B  32 " --> pdb=" O   TYR B  48 " (cutoff:3.500A)
      removed outlier: 4.864A  pdb=" N   TYR B  48 " --> pdb=" O   VAL B  32 " (cutoff:3.500A)
      removed outlier: 6.455A  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: 4.954A  pdb=" N   ALA B 127 " --> pdb=" O   ILE B 174 " (cutoff:3.500A)
      removed outlier: 7.236A  pdb=" N   ILE B 174 " --> pdb=" O   ALA B 127 " (cutoff:3.500A)
      removed outlier: 5.779A  pdb=" N   VAL B 129 " --> pdb=" O   LEU B 172 " (cutoff:3.500A)
      removed outlier: 7.182A  pdb=" N   LEU B 172 " --> pdb=" O   VAL B 129 " (cutoff:3.500A)
      removed outlier: 5.517A  pdb=" N   PHE B 131 " --> pdb=" O   ALA B 170 " (cutoff:3.500A)
      removed outlier: 7.226A  pdb=" N   ALA B 170 " --> pdb=" O   PHE B 131 " (cutoff:3.500A)
      removed outlier: 5.367A  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: 4.566A  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
    Processing sheet with id=AA6, first strand: chain 'C' and resid 56 through 58
      removed outlier: 5.514A  pdb=" N   TRP C  46 " --> pdb=" O   PHE C  38 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   PHE C  38 " --> pdb=" O   TRP C  46 " (cutoff:3.500A)
      removed outlier: 3.825A  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: 3.628A  pdb=" N   VAL C 176 " --> pdb=" O   LEU C 137 " (cutoff:3.500A)
      removed outlier: 5.920A  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: 3.628A  pdb=" N   VAL C 176 " --> pdb=" O   LEU C 137 " (cutoff:3.500A)
      removed outlier: 5.920A  pdb=" N   TRP C 170 " --> pdb=" O   GLY C 143 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 185 through 187

    392 hydrogen bonds defined for protein.
    1115 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: 1.67

  Time building geometry restraints manager: 1.79 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 964
        1.31 -     1.44: 1856
        1.44 -     1.56: 3666
        1.56 -     1.69: 36
        1.69 -     1.81: 42
  Bond restraints: 6564
  Sorted by residual:
  bond pdb=" C1B LMT A 609 "
       pdb=" O5B LMT A 609 "
    ideal  model  delta    sigma   weight residual
    1.393  1.517 -0.124 2.00e-02 2.50e+03 3.84e+01
  bond pdb=" C1B LMT A 606 "
       pdb=" O5B LMT A 606 "
    ideal  model  delta    sigma   weight residual
    1.393  1.517 -0.124 2.00e-02 2.50e+03 3.83e+01
  bond pdb=" C1B LMT A 605 "
       pdb=" O5B LMT A 605 "
    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 604 "
       pdb=" O5B LMT A 604 "
    ideal  model  delta    sigma   weight residual
    1.393  1.514 -0.121 2.00e-02 2.50e+03 3.68e+01
  bond pdb=" C1B LMT A 602 "
       pdb=" O5B LMT A 602 "
    ideal  model  delta    sigma   weight residual
    1.393  1.512 -0.119 2.00e-02 2.50e+03 3.57e+01
  ... (remaining 6559 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.29: 8869
        5.29 -    10.58: 109
       10.58 -    15.87: 5
       15.87 -    21.17: 2
       21.17 -    26.46: 4
  Bond angle restraints: 8989
  Sorted by residual:
  angle pdb=" N   GLY B  97 "
        pdb=" CA  GLY B  97 "
        pdb=" C   GLY B  97 "
      ideal   model   delta    sigma   weight residual
     113.18   86.72   26.46 2.37e+00 1.78e-01 1.25e+02
  angle pdb=" C03 ZGS A 601 "
        pdb=" C04 ZGS A 601 "
        pdb=" C05 ZGS A 601 "
      ideal   model   delta    sigma   weight residual
     127.34  152.42  -25.08 3.00e+00 1.11e-01 6.99e+01
  angle pdb=" C09 ZGS A 601 "
        pdb=" C10 ZGS A 601 "
        pdb=" C11 ZGS A 601 "
      ideal   model   delta    sigma   weight residual
     127.16  152.19  -25.03 3.00e+00 1.11e-01 6.96e+01
  angle pdb=" C06 ZGS A 601 "
        pdb=" C07 ZGS A 601 "
        pdb=" C08 ZGS A 601 "
      ideal   model   delta    sigma   weight residual
     127.52  152.28  -24.76 3.00e+00 1.11e-01 6.81e+01
  angle pdb=" C04 ZGS A 601 "
        pdb=" C05 ZGS A 601 "
        pdb=" C06 ZGS A 601 "
      ideal   model   delta    sigma   weight residual
     110.70  130.45  -19.75 3.00e+00 1.11e-01 4.33e+01
  ... (remaining 8984 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.37: 3655
       25.37 -    50.74: 199
       50.74 -    76.12: 72
       76.12 -   101.49: 58
      101.49 -   126.86: 74
  Dihedral angle restraints: 4058
    sinusoidal: 1598
      harmonic: 2460
  Sorted by residual:
  dihedral pdb=" C23 ZGS A 601 "
           pdb=" O24 ZGS A 601 "
           pdb=" P25 ZGS A 601 "
           pdb=" O28 ZGS A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
      66.18 -166.96 -126.86     1      3.00e+01 1.11e-03 1.71e+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 -174.52 -121.75     1      3.00e+01 1.11e-03 1.63e+01
  dihedral pdb=" C1B 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
    -175.52  -54.27 -121.25     1      3.00e+01 1.11e-03 1.62e+01
  ... (remaining 4055 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 858
       0.058 -    0.116: 176
       0.116 -    0.175: 29
       0.175 -    0.233: 6
       0.233 -    0.291: 1
  Chirality restraints: 1070
  Sorted by residual:
  chirality pdb=" C1B LMT A 607 "
            pdb=" C2B LMT A 607 "
            pdb=" O1B LMT A 607 "
            pdb=" O5B LMT A 607 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.20   -2.49    0.29 2.00e-01 2.50e+01 2.11e+00
  chirality pdb=" C4' LMT A 606 "
            pdb=" C3' LMT A 606 "
            pdb=" C5' LMT A 606 "
            pdb=" O1B LMT A 606 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.55   -2.33   -0.23 2.00e-01 2.50e+01 1.28e+00
  chirality pdb=" C1B LMT A 602 "
            pdb=" C2B LMT A 602 "
            pdb=" O1B LMT A 602 "
            pdb=" O5B LMT A 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.20   -2.40    0.20 2.00e-01 2.50e+01 1.01e+00
  ... (remaining 1067 not shown)

  Planarity restraints: 1105
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE C 103 "   -0.048 5.00e-02 4.00e+02   7.31e-02 8.55e+00
        pdb=" N   PRO C 104 "    0.126 5.00e-02 4.00e+02
        pdb=" CA  PRO C 104 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO C 104 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP C  46 "    0.043 5.00e-02 4.00e+02   6.55e-02 6.86e+00
        pdb=" N   PRO C  47 "   -0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO C  47 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO C  47 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B  75 "   -0.037 5.00e-02 4.00e+02   5.61e-02 5.03e+00
        pdb=" N   PRO B  76 "    0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO B  76 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B  76 "   -0.031 5.00e-02 4.00e+02
  ... (remaining 1102 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1524
        2.79 -     3.32: 5616
        3.32 -     3.84: 10714
        3.84 -     4.37: 11332
        4.37 -     4.90: 20286
  Nonbonded interactions: 49472
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN A  62 "
            pdb=" OG1 THR A 444 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" N   GLY B  97 "
            pdb=" O   GLY B  97 "
     model   vdw
     2.279 2.496
  nonbonded pdb=" OD2 ASP A  72 "
            pdb=" O6B LMT A 606 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" OH  TYR A 129 "
            pdb=" O4' LMT A 605 "
     model   vdw
     2.308 3.040
  nonbonded pdb=" O   VAL A 332 "
            pdb=" OG  SER A 336 "
     model   vdw
     2.310 3.040
  ... (remaining 49467 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=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.860
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     21.350
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.040
  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:3.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7256
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      :  0.010   0.124   6564  Z= 0.621
  Angle     :  1.275  26.456   8989  Z= 0.535
  Chirality :  0.051   0.291   1070
  Planarity :  0.007   0.073   1105
  Dihedral  : 28.636 126.860   2478
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.19 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  7.12 %
    Favored  : 92.13 %
  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: -1.27 (0.27), residues: 862
  helix:  0.05 (0.24), residues: 370
  sheet:  0.01 (0.39), residues: 188
  loop : -2.51 (0.31), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 140 
 HIS   0.001   0.000   HIS A 156 
 PHE   0.022   0.002   PHE B  89 
 TYR   0.018   0.002   TYR A  43 
 ARG   0.003   0.000   ARG A 237 

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 183
  time to evaluate  : 0.657 
Fit side-chains
REVERT: A  242 ILE cc_start: 0.8081 (mt) cc_final: 0.7616 (mm)
REVERT: B   70 SER cc_start: 0.8046 (t) cc_final: 0.7226 (m)
REVERT: B   72 SER cc_start: 0.8202 (m) cc_final: 0.7856 (p)
REVERT: B  154 MET cc_start: 0.8205 (mtt) cc_final: 0.7539 (mtm)
REVERT: B  156 TRP cc_start: 0.8406 (m-90) cc_final: 0.7857 (m-90)
REVERT: C   81 ILE cc_start: 0.7687 (mm) cc_final: 0.7456 (mt)
REVERT: C  136 THR cc_start: 0.9103 (m) cc_final: 0.8872 (p)
REVERT: C  190 PHE cc_start: 0.7268 (t80) cc_final: 0.7053 (t80)
  outliers start: 3
  outliers final: 0
  residues processed: 185
  average time/residue: 0.1651
  time to fit residues: 41.1055
Evaluate side-chains
  109 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    0.0020
   chunk 65 optimal weight:    8.9990
   chunk 36 optimal weight:    0.8980
   chunk 22 optimal weight:   30.0000
   chunk 43 optimal weight:    0.9980
   chunk 34 optimal weight:    0.5980
   chunk 67 optimal weight:    8.9990
   chunk 26 optimal weight:    0.5980
   chunk 40 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 78 optimal weight:    0.0270
   overall best weight:    0.4046

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

Flipped N/Q/H residues before XYZ refinement:
A  51 GLN
A 135 GLN
A 238 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.161793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.143289 restraints weight = 16336.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.141750 restraints weight = 21402.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.142932 restraints weight = 17440.199|
|-----------------------------------------------------------------------------|
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3656
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3656 r_free = 0.3656    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3655 r_free = 0.3655    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3655
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
moved from start:          0.2345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6564  Z= 0.219
  Angle     :  0.819  11.662   8989  Z= 0.367
  Chirality :  0.055   0.730   1070
  Planarity :  0.006   0.057   1105
  Dihedral  : 16.878 138.854   1430
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  2.06 %
    Favored  : 97.75 %
  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: -0.53 (0.28), residues: 862
  helix:  1.11 (0.26), residues: 372
  sheet: -0.01 (0.41), residues: 176
  loop : -2.41 (0.30), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 140 
 HIS   0.002   0.001   HIS A 230 
 PHE   0.031   0.002   PHE A 298 
 TYR   0.035   0.002   TYR A 358 
 ARG   0.004   0.000   ARG C  92 

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.664 
Fit side-chains
   revert: symmetry clash
REVERT: A  242 ILE cc_start: 0.8446 (mt) cc_final: 0.7944 (mm)
REVERT: A  369 ILE cc_start: 0.7956 (mm) cc_final: 0.7712 (mm)
REVERT: A  462 GLU cc_start: 0.7464 (mp0) cc_final: 0.7173 (mt-10)
REVERT: B   70 SER cc_start: 0.8607 (t) cc_final: 0.8048 (m)
REVERT: B   88 LEU cc_start: 0.8186 (pp) cc_final: 0.7225 (mp)
REVERT: C   81 ILE cc_start: 0.7971 (mm) cc_final: 0.7683 (mm)
REVERT: C   93 CYS cc_start: 0.5998 (t) cc_final: 0.5709 (t)
REVERT: C  112 ASN cc_start: 0.7482 (p0) cc_final: 0.7167 (p0)
REVERT: C  136 THR cc_start: 0.8655 (m) cc_final: 0.8451 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.1497
  time to fit residues: 29.1910
Evaluate side-chains
  109 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.653 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 75 optimal weight:    0.7980
   chunk 53 optimal weight:    0.0370
   chunk 50 optimal weight:    1.9990
   chunk 26 optimal weight:    0.5980
   chunk 32 optimal weight:    0.1980
   chunk 72 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 67 optimal weight:    7.9990
   chunk 79 optimal weight:    7.9990
   chunk 47 optimal weight:    0.0270
   overall best weight:    0.3316

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

Flipped N/Q/H residues before XYZ refinement:
A 328 ASN
B 134 ASN
B 153 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.162400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.150103 restraints weight = 29469.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.149000 restraints weight = 29930.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.147624 restraints weight = 13997.867|
|-----------------------------------------------------------------------------|
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3696
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3696 r_free = 0.3696    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3696 r_free = 0.3696    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3696
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7435
moved from start:          0.2647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6564  Z= 0.181
  Angle     :  0.661   7.090   8989  Z= 0.313
  Chirality :  0.045   0.288   1070
  Planarity :  0.006   0.063   1105
  Dihedral  : 12.758 130.568   1430
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  1.12 %
    Favored  : 98.69 %
  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: 862
  helix:  1.38 (0.26), residues: 376
  sheet:  0.22 (0.40), residues: 195
  loop : -2.21 (0.33), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B 135 
 HIS   0.000   0.000   HIS A 156 
 PHE   0.024   0.002   PHE A 298 
 TYR   0.016   0.002   TYR C 123 
 ARG   0.003   0.000   ARG C  13 

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.500 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  242 ILE cc_start: 0.8244 (mt) cc_final: 0.7802 (mm)
REVERT: A  369 ILE cc_start: 0.7971 (mm) cc_final: 0.7744 (mm)
REVERT: B   70 SER cc_start: 0.8524 (t) cc_final: 0.7949 (m)
REVERT: B   88 LEU cc_start: 0.8181 (pp) cc_final: 0.7188 (mp)
REVERT: C   81 ILE cc_start: 0.8026 (mm) cc_final: 0.7642 (mm)
REVERT: C  136 THR cc_start: 0.8718 (m) cc_final: 0.8472 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 134
  average time/residue: 0.1557
  time to fit residues: 28.4783
Evaluate side-chains
  102 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 66 optimal weight:    4.9990
   chunk 1 optimal weight:    0.8980
   chunk 55 optimal weight:    0.3980
   chunk 53 optimal weight:    1.9990
   chunk 54 optimal weight:    0.8980
   chunk 2 optimal weight:    0.5980
   chunk 34 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0020
   chunk 18 optimal weight:    0.0570
   chunk 76 optimal weight:    0.0970
   overall best weight:    0.2304

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.163993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.149593 restraints weight = 28247.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.150049 restraints weight = 33571.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.149021 restraints weight = 11933.099|
|-----------------------------------------------------------------------------|
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3714
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3714 r_free = 0.3714    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3714 r_free = 0.3714    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3714
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7409
moved from start:          0.2960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6564  Z= 0.164
  Angle     :  0.622   6.625   8989  Z= 0.299
  Chirality :  0.042   0.255   1070
  Planarity :  0.005   0.055   1105
  Dihedral  : 11.741 123.802   1430
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  0.75 %
    Favored  : 99.06 %
  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: 862
  helix:  1.63 (0.26), residues: 374
  sheet: -0.01 (0.43), residues: 169
  loop : -2.03 (0.31), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 344 
 HIS   0.001   0.000   HIS A 156 
 PHE   0.031   0.002   PHE A 486 
 TYR   0.014   0.001   TYR A 291 
 ARG   0.003   0.000   ARG B 191 

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.683 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 THR cc_start: 0.8627 (p) cc_final: 0.8354 (t)
REVERT: A  242 ILE cc_start: 0.8339 (mt) cc_final: 0.8036 (mm)
REVERT: A  294 LEU cc_start: 0.8435 (tp) cc_final: 0.7990 (tt)
REVERT: A  334 MET cc_start: 0.7575 (mmm) cc_final: 0.7361 (mmp)
REVERT: A  369 ILE cc_start: 0.8009 (mm) cc_final: 0.7795 (mm)
REVERT: B   70 SER cc_start: 0.8479 (t) cc_final: 0.7978 (m)
REVERT: B   88 LEU cc_start: 0.8083 (pp) cc_final: 0.7157 (mp)
REVERT: C   81 ILE cc_start: 0.8041 (mm) cc_final: 0.7734 (mm)
REVERT: C  136 THR cc_start: 0.8721 (m) cc_final: 0.8456 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.1560
  time to fit residues: 28.0641
Evaluate side-chains
  105 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 77 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 0 optimal weight:    9.9990
   chunk 40 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 32 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 37 optimal weight:    0.1980
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
B 159 GLN
C  99 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.157840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.143286 restraints weight = 37236.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.145186 restraints weight = 35300.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.145825 restraints weight = 10885.357|
|-----------------------------------------------------------------------------|
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3682
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3682 r_free = 0.3682    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3682 r_free = 0.3682    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3682
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7490
moved from start:          0.3091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6564  Z= 0.256
  Angle     :  0.684   6.554   8989  Z= 0.334
  Chirality :  0.045   0.255   1070
  Planarity :  0.005   0.057   1105
  Dihedral  : 11.615 121.360   1430
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  2.62 %
    Favored  : 97.19 %
  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: 862
  helix:  1.59 (0.27), residues: 376
  sheet: -0.01 (0.41), residues: 178
  loop : -2.05 (0.32), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP C  95 
 HIS   0.001   0.000   HIS A 156 
 PHE   0.028   0.002   PHE A 431 
 TYR   0.028   0.002   TYR A 358 
 ARG   0.005   0.001   ARG C  13 

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.627 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 THR cc_start: 0.8640 (p) cc_final: 0.8432 (t)
REVERT: A  242 ILE cc_start: 0.8333 (mt) cc_final: 0.8050 (mm)
REVERT: A  369 ILE cc_start: 0.8039 (mm) cc_final: 0.7824 (mm)
REVERT: B   70 SER cc_start: 0.8630 (t) cc_final: 0.8054 (m)
REVERT: B   88 LEU cc_start: 0.8228 (pp) cc_final: 0.7200 (mp)
REVERT: C   81 ILE cc_start: 0.8083 (mm) cc_final: 0.7690 (mm)
REVERT: C  136 THR cc_start: 0.8746 (m) cc_final: 0.8445 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.1554
  time to fit residues: 26.7567
Evaluate side-chains
  103 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 83 optimal weight:    0.8980
   chunk 11 optimal weight:    0.6980
   chunk 57 optimal weight:    0.1980
   chunk 29 optimal weight:    0.9980
   chunk 22 optimal weight:   30.0000
   chunk 23 optimal weight:    6.9990
   chunk 54 optimal weight:    0.9980
   chunk 18 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9980
   chunk 59 optimal weight:    0.6980
   chunk 79 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 159 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.157924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.143674 restraints weight = 34716.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.144747 restraints weight = 34839.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.144195 restraints weight = 11761.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3647
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3647 r_free = 0.3647    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3647 r_free = 0.3647    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3647
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.3236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6564  Z= 0.226
  Angle     :  0.651   6.681   8989  Z= 0.318
  Chirality :  0.043   0.253   1070
  Planarity :  0.005   0.057   1105
  Dihedral  : 11.269 118.840   1430
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  2.25 %
    Favored  : 97.57 %
  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: -0.04 (0.29), residues: 862
  helix:  1.51 (0.27), residues: 376
  sheet: -0.04 (0.40), residues: 180
  loop : -2.02 (0.33), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C  95 
 HIS   0.000   0.000   HIS A 156 
 PHE   0.023   0.002   PHE A 431 
 TYR   0.026   0.002   TYR A 291 
 ARG   0.004   0.000   ARG B 191 

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.662 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 LEU cc_start: 0.6312 (tp) cc_final: 0.5920 (tt)
REVERT: A  294 LEU cc_start: 0.8417 (tp) cc_final: 0.8055 (tt)
REVERT: B   70 SER cc_start: 0.8584 (t) cc_final: 0.8009 (m)
REVERT: B   88 LEU cc_start: 0.8095 (pp) cc_final: 0.7302 (mp)
REVERT: C   81 ILE cc_start: 0.8083 (mm) cc_final: 0.7705 (mt)
REVERT: C  136 THR cc_start: 0.8777 (m) cc_final: 0.8438 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.1464
  time to fit residues: 25.9785
Evaluate side-chains
  103 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9990
   chunk 62 optimal weight:    0.0770
   chunk 59 optimal weight:    0.3980
   chunk 12 optimal weight:    0.9980
   chunk 57 optimal weight:    0.0980
   chunk 38 optimal weight:    0.3980
   chunk 28 optimal weight:    0.6980
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.3338

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.159991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.147317 restraints weight = 34714.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.147244 restraints weight = 30291.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.145799 restraints weight = 11450.394|
|-----------------------------------------------------------------------------|
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3670
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3670 r_free = 0.3670    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3670 r_free = 0.3670    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3670
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7476
moved from start:          0.3355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6564  Z= 0.174
  Angle     :  0.635   6.629   8989  Z= 0.308
  Chirality :  0.043   0.251   1070
  Planarity :  0.005   0.054   1105
  Dihedral  : 10.921 116.232   1430
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  1.12 %
    Favored  : 98.69 %
  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:  0.00 (0.29), residues: 862
  helix:  1.52 (0.26), residues: 380
  sheet:  0.05 (0.40), residues: 178
  loop : -2.05 (0.33), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C 106 
 HIS   0.000   0.000   HIS A 156 
 PHE   0.031   0.002   PHE A 431 
 TYR   0.034   0.002   TYR A 358 
 ARG   0.004   0.000   ARG B 191 

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.643 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 MET cc_start: 0.7355 (mmm) cc_final: 0.6892 (tpt)
REVERT: A  315 PHE cc_start: 0.7840 (t80) cc_final: 0.7538 (t80)
REVERT: A  369 ILE cc_start: 0.8191 (mm) cc_final: 0.7914 (mm)
REVERT: B   70 SER cc_start: 0.8492 (t) cc_final: 0.7997 (m)
REVERT: B   88 LEU cc_start: 0.8133 (pp) cc_final: 0.7267 (mp)
REVERT: B  120 LEU cc_start: 0.7139 (tt) cc_final: 0.6483 (tp)
REVERT: C   81 ILE cc_start: 0.8088 (mm) cc_final: 0.7687 (mm)
REVERT: C   93 CYS cc_start: 0.5859 (t) cc_final: 0.5631 (t)
REVERT: C  136 THR cc_start: 0.8729 (m) cc_final: 0.8369 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.1477
  time to fit residues: 25.6540
Evaluate side-chains
  104 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.611 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 58 optimal weight:    0.0040
   chunk 85 optimal weight:    0.7980
   chunk 17 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 65 optimal weight:    0.0770
   chunk 22 optimal weight:   50.0000
   chunk 15 optimal weight:    0.8980
   chunk 43 optimal weight:    0.5980
   chunk 26 optimal weight:    0.5980
   chunk 23 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   overall best weight:    0.3950

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.160382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.148270 restraints weight = 31698.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.146315 restraints weight = 30965.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.144660 restraints weight = 13350.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3641
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3641 r_free = 0.3641    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3641 r_free = 0.3641    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3641
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7519
moved from start:          0.3500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6564  Z= 0.180
  Angle     :  0.628   6.716   8989  Z= 0.305
  Chirality :  0.043   0.246   1070
  Planarity :  0.005   0.054   1105
  Dihedral  : 10.632 114.810   1430
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  1.12 %
    Favored  : 98.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.29), residues: 862
  helix:  1.60 (0.27), residues: 380
  sheet: -0.03 (0.40), residues: 180
  loop : -1.97 (0.33), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP C  46 
 HIS   0.000   0.000   HIS A 156 
 PHE   0.028   0.002   PHE A 431 
 TYR   0.022   0.002   TYR C 123 
 ARG   0.006   0.000   ARG B 191 

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.721 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 MET cc_start: 0.7462 (mmm) cc_final: 0.7218 (tpt)
REVERT: A  315 PHE cc_start: 0.7852 (t80) cc_final: 0.7573 (t80)
REVERT: A  333 ILE cc_start: 0.8764 (mm) cc_final: 0.8514 (mm)
REVERT: A  369 ILE cc_start: 0.8240 (mm) cc_final: 0.7981 (mm)
REVERT: B   70 SER cc_start: 0.8464 (t) cc_final: 0.7918 (m)
REVERT: B   88 LEU cc_start: 0.8136 (pp) cc_final: 0.7297 (mp)
REVERT: B  120 LEU cc_start: 0.7068 (tt) cc_final: 0.6340 (tp)
REVERT: C   81 ILE cc_start: 0.8070 (mm) cc_final: 0.7798 (mm)
REVERT: C  136 THR cc_start: 0.8763 (m) cc_final: 0.8386 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 125
  average time/residue: 0.1567
  time to fit residues: 27.4897
Evaluate side-chains
  104 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 2 optimal weight:    0.9980
   chunk 60 optimal weight:    0.0070
   chunk 48 optimal weight:    0.4980
   chunk 24 optimal weight:    3.9990
   chunk 50 optimal weight:    0.4980
   chunk 65 optimal weight:    7.9990
   chunk 84 optimal weight:    9.9990
   chunk 41 optimal weight:    0.0370
   chunk 4 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.3476

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.161424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.149359 restraints weight = 27187.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.146557 restraints weight = 28352.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.144974 restraints weight = 12748.608|
|-----------------------------------------------------------------------------|
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3627
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3627 r_free = 0.3627    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3627 r_free = 0.3627    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3627
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
moved from start:          0.3554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6564  Z= 0.171
  Angle     :  0.620   6.614   8989  Z= 0.303
  Chirality :  0.042   0.243   1070
  Planarity :  0.005   0.055   1105
  Dihedral  : 10.382 112.914   1430
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  1.12 %
    Favored  : 98.69 %
  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:  0.12 (0.29), residues: 862
  helix:  1.67 (0.26), residues: 380
  sheet: -0.01 (0.41), residues: 178
  loop : -1.98 (0.33), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C  46 
 HIS   0.000   0.000   HIS A 156 
 PHE   0.026   0.001   PHE A 431 
 TYR   0.011   0.001   TYR A 291 
 ARG   0.006   0.000   ARG B 191 

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.624 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 MET cc_start: 0.7345 (mmm) cc_final: 0.6989 (tpt)
REVERT: A  315 PHE cc_start: 0.7840 (t80) cc_final: 0.7563 (t80)
REVERT: A  369 ILE cc_start: 0.8188 (mm) cc_final: 0.7960 (mm)
REVERT: B   70 SER cc_start: 0.8491 (t) cc_final: 0.7984 (m)
REVERT: B   88 LEU cc_start: 0.8090 (pp) cc_final: 0.7282 (mp)
REVERT: B  120 LEU cc_start: 0.7156 (tt) cc_final: 0.6623 (tp)
REVERT: C   81 ILE cc_start: 0.8067 (mm) cc_final: 0.7685 (mt)
REVERT: C  136 THR cc_start: 0.8770 (m) cc_final: 0.8416 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 121
  average time/residue: 0.1448
  time to fit residues: 24.4455
Evaluate side-chains
  104 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.670 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 65 optimal weight:    7.9990
   chunk 7 optimal weight:    5.9990
   chunk 4 optimal weight:    0.6980
   chunk 29 optimal weight:    0.3980
   chunk 80 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 14 optimal weight:    0.7980
   chunk 71 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
B  37 GLN
C  39 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.157479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.144562 restraints weight = 34167.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.144602 restraints weight = 31415.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.143307 restraints weight = 10972.218|
|-----------------------------------------------------------------------------|
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3635
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3635 r_free = 0.3635    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3635 r_free = 0.3635    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3635
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7544
moved from start:          0.3617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6564  Z= 0.253
  Angle     :  0.672   6.720   8989  Z= 0.330
  Chirality :  0.044   0.241   1070
  Planarity :  0.005   0.056   1105
  Dihedral  : 10.508 113.784   1430
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.96 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  0.56 %
    Favored  : 99.25 %
  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: 862
  helix:  1.58 (0.27), residues: 378
  sheet: -0.24 (0.40), residues: 180
  loop : -1.94 (0.33), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP C  46 
 HIS   0.001   0.000   HIS A 156 
 PHE   0.029   0.002   PHE A 431 
 TYR   0.026   0.002   TYR A 291 
 ARG   0.005   0.001   ARG B 191 

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.615 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 LEU cc_start: 0.6300 (tp) cc_final: 0.5937 (tt)
REVERT: A  103 TRP cc_start: 0.7887 (t60) cc_final: 0.7552 (t-100)
REVERT: A  315 PHE cc_start: 0.7969 (t80) cc_final: 0.7674 (t80)
REVERT: A  369 ILE cc_start: 0.8276 (mm) cc_final: 0.8019 (mm)
REVERT: B   70 SER cc_start: 0.8565 (t) cc_final: 0.7995 (m)
REVERT: B   88 LEU cc_start: 0.8151 (pp) cc_final: 0.7413 (mp)
REVERT: B  139 ILE cc_start: 0.7989 (tt) cc_final: 0.6838 (tt)
REVERT: C   81 ILE cc_start: 0.8085 (mm) cc_final: 0.7705 (mt)
REVERT: C  136 THR cc_start: 0.8744 (m) cc_final: 0.8394 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.1496
  time to fit residues: 25.9595
Evaluate side-chains
  106 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.660 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 23 optimal weight:    0.6980
   chunk 42 optimal weight:    0.0030
   chunk 11 optimal weight:    0.8980
   chunk 75 optimal weight:    0.1980
   chunk 21 optimal weight:    0.9990
   chunk 7 optimal weight:    0.1980
   chunk 59 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   chunk 73 optimal weight:    4.9990
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.3590

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

Flipped N/Q/H residues before XYZ refinement:
A 328 ASN
B  37 GLN
C  39 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.161179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.148546 restraints weight = 31648.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.147853 restraints weight = 30468.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.146971 restraints weight = 11583.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3680
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3680 r_free = 0.3680    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3680 r_free = 0.3680    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3680
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7478
moved from start:          0.3721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6564  Z= 0.189
  Angle     :  0.641   6.908   8989  Z= 0.313
  Chirality :  0.042   0.243   1070
  Planarity :  0.005   0.056   1105
  Dihedral  : 10.288 112.463   1430
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  0.37 %
    Favored  : 99.44 %
  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: 862
  helix:  1.59 (0.27), residues: 380
  sheet: -0.20 (0.40), residues: 178
  loop : -1.96 (0.33), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.002   TRP A 112 
 HIS   0.001   0.000   HIS A 156 
 PHE   0.028   0.001   PHE A 431 
 TYR   0.022   0.002   TYR A 358 
 ARG   0.006   0.001   ARG B 191 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2241.53 seconds
wall clock time: 40 minutes 58.43 seconds (2458.43 seconds total)