Starting phenix.real_space_refine
on Wed Mar 12 12:56:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d2v_27151/03_2025/8d2v_27151.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d2v_27151/03_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_27151/03_2025/8d2v_27151.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d2v_27151/03_2025/8d2v_27151.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d2v_27151/03_2025/8d2v_27151.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d2v_27151/03_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-5624/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: 6.82, per 1000 atoms: 1.07
  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: 1.68
  Conformation dependent library (CDL) restraints added in 1.3 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: 0.67
  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: 1.84

  Time building geometry restraints manager: 1.91 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:             3.660
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     21.610
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.620
-------------------------------------------------------------------------------
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  : 0.759 
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: 0.1820
  time to fit residues: 45.5553
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  : 0.685 
-------------------------------------------------------------------------------
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 = 0.143282 restraints weight = 16336.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.141532 restraints weight = 21731.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.142976 restraints weight = 18106.787|
|-----------------------------------------------------------------------------|
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: 0.7523
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  : 0.614 
Fit side-chains
   revert: symmetry clash
REVERT: A  242 ILE cc_start: 0.8441 (mt) cc_final: 0.7939 (mm)
REVERT: A  369 ILE cc_start: 0.7958 (mm) cc_final: 0.7714 (mm)
REVERT: A  462 GLU cc_start: 0.7464 (mp0) cc_final: 0.7174 (mt-10)
REVERT: B   70 SER cc_start: 0.8618 (t) cc_final: 0.8059 (m)
REVERT: B   88 LEU cc_start: 0.8176 (pp) cc_final: 0.7216 (mp)
REVERT: C   81 ILE cc_start: 0.7973 (mm) cc_final: 0.7685 (mm)
REVERT: C   93 CYS cc_start: 0.6005 (t) cc_final: 0.5713 (t)
REVERT: C  112 ASN cc_start: 0.7485 (p0) cc_final: 0.7168 (p0)
REVERT: C  136 THR cc_start: 0.8657 (m) cc_final: 0.8453 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.1403
  time to fit residues: 27.5369
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  : 0.607 
-------------------------------------------------------------------------------
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:    0.9990
   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:    5.9990
   chunk 47 optimal weight:    0.0570
   overall best weight:    0.3778

-------------------------------------------------------------------------------
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 = 0.3885 r_free = 0.3885 target = 0.161870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.149801 restraints weight = 29411.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.147075 restraints weight = 29536.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.145393 restraints weight = 14096.494|
|-----------------------------------------------------------------------------|
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3645
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3645 r_free = 0.3645    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 = 0.3645 r_free = 0.3645    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3645
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7520
moved from start:          0.2648

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= 0.186
  Angle     :  0.665   7.087   8989  Z= 0.315
  Chirality :  0.045   0.287   1070
  Planarity :  0.006   0.067   1105
  Dihedral  : 12.755 130.390   1430
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  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:  1.38 (0.26), residues: 376
  sheet:  0.18 (0.40), residues: 196
  loop : -2.17 (0.33), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 135 
 HIS   0.000   0.000   HIS A 156 
 PHE   0.024   0.002   PHE A 298 
 TYR   0.017   0.002   TYR C 123 
 ARG   0.004   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
  135 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.693 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  242 ILE cc_start: 0.8245 (mt) cc_final: 0.7805 (mm)
REVERT: A  369 ILE cc_start: 0.8022 (mm) cc_final: 0.7804 (mm)
REVERT: B   70 SER cc_start: 0.8553 (t) cc_final: 0.8012 (m)
REVERT: B   88 LEU cc_start: 0.8197 (pp) cc_final: 0.7193 (mp)
REVERT: C   81 ILE cc_start: 0.8036 (mm) cc_final: 0.7645 (mm)
REVERT: C  136 THR cc_start: 0.8805 (m) cc_final: 0.8556 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.1706
  time to fit residues: 32.5616
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  : 0.667 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 1 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   chunk 2 optimal weight:    0.6980
   chunk 34 optimal weight:    0.8980
   chunk 46 optimal weight:    0.2980
   chunk 13 optimal weight:    0.0270
   chunk 18 optimal weight:    0.0060
   chunk 76 optimal weight:    0.7980
   overall best weight:    0.3654

-------------------------------------------------------------------------------
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 = 0.3891 r_free = 0.3891 target = 0.162503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.149754 restraints weight = 29309.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.148420 restraints weight = 29910.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.147220 restraints weight = 12555.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3675
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3675 r_free = 0.3675    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 = 0.3675 r_free = 0.3675    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3675
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7470
moved from start:          0.2936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6564  Z= 0.181
  Angle     :  0.635   6.639   8989  Z= 0.306
  Chirality :  0.043   0.257   1070
  Planarity :  0.005   0.056   1105
  Dihedral  : 11.865 124.060   1430
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  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:  0.02 (0.29), residues: 862
  helix:  1.59 (0.27), residues: 374
  sheet:  0.09 (0.42), residues: 178
  loop : -2.06 (0.32), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 106 
 HIS   0.001   0.000   HIS A 156 
 PHE   0.030   0.002   PHE A 486 
 TYR   0.016   0.001   TYR A 291 
 ARG   0.005   0.000   ARG C  92 

*********************** 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  : 0.678 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 THR cc_start: 0.8637 (p) cc_final: 0.8380 (t)
REVERT: A  242 ILE cc_start: 0.8295 (mt) cc_final: 0.7979 (mm)
REVERT: A  369 ILE cc_start: 0.8037 (mm) cc_final: 0.7821 (mm)
REVERT: A  421 GLU cc_start: 0.5787 (tt0) cc_final: 0.5512 (tm-30)
REVERT: B   70 SER cc_start: 0.8545 (t) cc_final: 0.8019 (m)
REVERT: B   88 LEU cc_start: 0.8110 (pp) cc_final: 0.6971 (mp)
REVERT: B  154 MET cc_start: 0.7660 (mtm) cc_final: 0.7459 (mtm)
REVERT: C   81 ILE cc_start: 0.7979 (mm) cc_final: 0.7646 (mm)
REVERT: C   93 CYS cc_start: 0.5812 (t) cc_final: 0.5572 (t)
REVERT: C  136 THR cc_start: 0.8793 (m) cc_final: 0.8528 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.1521
  time to fit residues: 27.3986
Evaluate side-chains
  108 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.641 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 40 optimal weight:    0.9980
   chunk 7 optimal weight:    0.0970
   chunk 32 optimal weight:    7.9990
   chunk 33 optimal weight:    0.0870
   chunk 19 optimal weight:    2.9990
   chunk 2 optimal weight:    0.5980
   chunk 8 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0870
   overall best weight:    0.3734

-------------------------------------------------------------------------------
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 = 0.3885 r_free = 0.3885 target = 0.161901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.148902 restraints weight = 36481.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.148960 restraints weight = 31908.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.147508 restraints weight = 11669.881|
|-----------------------------------------------------------------------------|
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3686
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3686 r_free = 0.3686    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 = 0.3686 r_free = 0.3686    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3686
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7446
moved from start:          0.3127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6564  Z= 0.178
  Angle     :  0.631   6.672   8989  Z= 0.303
  Chirality :  0.043   0.254   1070
  Planarity :  0.005   0.055   1105
  Dihedral  : 11.326 120.006   1430
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  1.50 %
    Favored  : 98.31 %
  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:  1.61 (0.27), residues: 379
  sheet:  0.15 (0.41), residues: 176
  loop : -2.08 (0.32), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C  95 
 HIS   0.000   0.000   HIS A 156 
 PHE   0.021   0.002   PHE A 431 
 TYR   0.032   0.002   TYR A 358 
 ARG   0.004   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
  126 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.706 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 THR cc_start: 0.8586 (p) cc_final: 0.8375 (t)
REVERT: A  242 ILE cc_start: 0.8315 (mt) cc_final: 0.8027 (mm)
REVERT: A  369 ILE cc_start: 0.8063 (mm) cc_final: 0.7848 (mm)
REVERT: B   70 SER cc_start: 0.8524 (t) cc_final: 0.7954 (m)
REVERT: B   88 LEU cc_start: 0.8083 (pp) cc_final: 0.7166 (mp)
REVERT: C   81 ILE cc_start: 0.8029 (mm) cc_final: 0.7608 (mm)
REVERT: C  136 THR cc_start: 0.8756 (m) cc_final: 0.8454 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.1528
  time to fit residues: 27.6241
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  : 0.664 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 11 optimal weight:    0.5980
   chunk 57 optimal weight:    0.0370
   chunk 29 optimal weight:    0.9990
   chunk 22 optimal weight:   50.0000
   chunk 23 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 6 optimal weight:    0.5980
   chunk 59 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9990
   overall best weight:    0.6258

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

Flipped N/Q/H residues before XYZ refinement:
A 238 ASN
B  37 GLN
B 159 GLN
C  39 GLN
C  99 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.159422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.146565 restraints weight = 35010.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.146427 restraints weight = 32306.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.144936 restraints weight = 12121.208|
|-----------------------------------------------------------------------------|
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3658
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3658 r_free = 0.3658    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 = 0.3658 r_free = 0.3658    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3658
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7503
moved from start:          0.3227

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= 0.220
  Angle     :  0.648   6.853   8989  Z= 0.315
  Chirality :  0.043   0.249   1070
  Planarity :  0.005   0.055   1105
  Dihedral  : 11.104 118.693   1430
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  1.31 %
    Favored  : 98.50 %
  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:  1.54 (0.27), residues: 376
  sheet: -0.00 (0.41), residues: 178
  loop : -1.99 (0.32), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP C  95 
 HIS   0.000   0.000   HIS A 156 
 PHE   0.027   0.002   PHE A 431 
 TYR   0.026   0.002   TYR A 291 
 ARG   0.005   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
  126 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.609 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 THR cc_start: 0.8627 (p) cc_final: 0.8345 (t)
REVERT: A  110 MET cc_start: 0.7028 (tpt) cc_final: 0.6692 (tmm)
REVERT: A  242 ILE cc_start: 0.8344 (mt) cc_final: 0.8085 (mm)
REVERT: A  333 ILE cc_start: 0.8820 (mm) cc_final: 0.8563 (mm)
REVERT: B   70 SER cc_start: 0.8613 (t) cc_final: 0.8024 (m)
REVERT: B   88 LEU cc_start: 0.8179 (pp) cc_final: 0.7277 (mp)
REVERT: B  120 LEU cc_start: 0.7218 (tt) cc_final: 0.6986 (tt)
REVERT: C   81 ILE cc_start: 0.8103 (mm) cc_final: 0.7705 (mm)
REVERT: C  136 THR cc_start: 0.8744 (m) cc_final: 0.8404 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.1438
  time to fit residues: 25.3608
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  : 0.586 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 53 optimal weight:    1.9990
   chunk 69 optimal weight:    0.6980
   chunk 52 optimal weight:    0.7980
   chunk 62 optimal weight:    4.9990
   chunk 59 optimal weight:    4.9990
   chunk 12 optimal weight:    0.6980
   chunk 57 optimal weight:    0.0980
   chunk 38 optimal weight:    0.9980
   chunk 28 optimal weight:    0.5980
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.3859 r_free = 0.3859 target = 0.159295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.146023 restraints weight = 34751.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.145806 restraints weight = 32841.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.144313 restraints weight = 13084.182|
|-----------------------------------------------------------------------------|
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3650
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3650 r_free = 0.3650    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3650 r_free = 0.3650    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3650
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
moved from start:          0.3318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6564  Z= 0.202
  Angle     :  0.637   6.683   8989  Z= 0.310
  Chirality :  0.043   0.247   1070
  Planarity :  0.005   0.054   1105
  Dihedral  : 10.849 116.956   1430
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  1.69 %
    Favored  : 98.13 %
  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:  0.02 (0.29), residues: 862
  helix:  1.53 (0.27), residues: 380
  sheet:  0.07 (0.40), residues: 176
  loop : -2.03 (0.33), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP C  95 
 HIS   0.000   0.000   HIS A 156 
 PHE   0.020   0.002   PHE A 431 
 TYR   0.035   0.002   TYR A 358 
 ARG   0.005   0.001   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
  127 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.599 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 THR cc_start: 0.8585 (p) cc_final: 0.8373 (t)
REVERT: A  242 ILE cc_start: 0.8373 (mt) cc_final: 0.8031 (mm)
REVERT: A  369 ILE cc_start: 0.8203 (mm) cc_final: 0.7899 (mm)
REVERT: A  385 SER cc_start: 0.7599 (t) cc_final: 0.7387 (p)
REVERT: B   70 SER cc_start: 0.8585 (t) cc_final: 0.8028 (m)
REVERT: B   88 LEU cc_start: 0.8195 (pp) cc_final: 0.7303 (mp)
REVERT: C   81 ILE cc_start: 0.8060 (mm) cc_final: 0.7714 (mm)
REVERT: C  136 THR cc_start: 0.8729 (m) cc_final: 0.8371 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.1509
  time to fit residues: 26.9227
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  : 0.682 
-------------------------------------------------------------------------------
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:    0.0670
   chunk 85 optimal weight:    7.9990
   chunk 17 optimal weight:    2.9990
   chunk 2 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9990
   chunk 22 optimal weight:   30.0000
   chunk 15 optimal weight:    0.6980
   chunk 43 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9980
   chunk 23 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.5118

-------------------------------------------------------------------------------
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 = 0.3857 r_free = 0.3857 target = 0.159350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.147062 restraints weight = 31820.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.146298 restraints weight = 30256.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.145045 restraints weight = 11349.233|
|-----------------------------------------------------------------------------|
r_work (final): 0.3661
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3661
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3661 r_free = 0.3661    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 = 0.3661 r_free = 0.3661    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3661
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7482
moved from start:          0.3496

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= 0.199
  Angle     :  0.644   6.730   8989  Z= 0.313
  Chirality :  0.043   0.244   1070
  Planarity :  0.005   0.054   1105
  Dihedral  : 10.667 115.699   1430
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  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:  0.01 (0.29), residues: 862
  helix:  1.53 (0.26), residues: 379
  sheet: -0.02 (0.40), residues: 178
  loop : -1.99 (0.33), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP C  46 
 HIS   0.000   0.000   HIS A 156 
 PHE   0.039   0.002   PHE A 431 
 TYR   0.015   0.002   TYR A 291 
 ARG   0.005   0.001   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
  128 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.689 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 THR cc_start: 0.8575 (p) cc_final: 0.8366 (t)
REVERT: A  242 ILE cc_start: 0.8393 (mt) cc_final: 0.8125 (mm)
REVERT: A  294 LEU cc_start: 0.8272 (tp) cc_final: 0.8014 (tt)
REVERT: A  369 ILE cc_start: 0.8181 (mm) cc_final: 0.7916 (mm)
REVERT: B   70 SER cc_start: 0.8528 (t) cc_final: 0.7995 (m)
REVERT: B   88 LEU cc_start: 0.8196 (pp) cc_final: 0.7377 (mp)
REVERT: B  139 ILE cc_start: 0.7918 (tt) cc_final: 0.6926 (tt)
REVERT: C   81 ILE cc_start: 0.8066 (mm) cc_final: 0.7686 (mt)
REVERT: C  136 THR cc_start: 0.8702 (m) cc_final: 0.8327 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.1528
  time to fit residues: 28.1338
Evaluate side-chains
  108 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 48 optimal weight:    0.7980
   chunk 24 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9990
   chunk 65 optimal weight:    0.0270
   chunk 84 optimal weight:    9.9990
   chunk 41 optimal weight:    0.7980
   chunk 4 optimal weight:    0.6980
   chunk 9 optimal weight:    0.5980
   chunk 20 optimal weight:    0.5980
   overall best weight:    0.5438

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

Flipped N/Q/H residues before XYZ refinement:
A 328 ASN
B 159 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.158954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.146951 restraints weight = 27246.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.144226 restraints weight = 26630.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.142320 restraints weight = 12725.674|
|-----------------------------------------------------------------------------|
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3602
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3602 r_free = 0.3602    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3602 r_free = 0.3602    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3602
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.3528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6564  Z= 0.202
  Angle     :  0.647   7.998   8989  Z= 0.314
  Chirality :  0.043   0.242   1070
  Planarity :  0.005   0.054   1105
  Dihedral  : 10.508 114.552   1430
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  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: -0.05 (0.29), residues: 862
  helix:  1.54 (0.27), residues: 380
  sheet: -0.19 (0.40), residues: 178
  loop : -2.00 (0.33), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP C  46 
 HIS   0.000   0.000   HIS A 156 
 PHE   0.032   0.002   PHE A 431 
 TYR   0.012   0.001   TYR A 291 
 ARG   0.005   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
  123 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.609 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 LEU cc_start: 0.6468 (tp) cc_final: 0.6082 (tt)
REVERT: A  242 ILE cc_start: 0.8369 (mt) cc_final: 0.8154 (mm)
REVERT: A  369 ILE cc_start: 0.8251 (mm) cc_final: 0.7983 (mm)
REVERT: B   70 SER cc_start: 0.8480 (t) cc_final: 0.7873 (m)
REVERT: B  120 LEU cc_start: 0.7135 (tt) cc_final: 0.6480 (tp)
REVERT: C   81 ILE cc_start: 0.8066 (mm) cc_final: 0.7650 (mt)
REVERT: C  136 THR cc_start: 0.8792 (m) cc_final: 0.8418 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 123
  average time/residue: 0.1415
  time to fit residues: 24.6200
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  : 0.597 
-------------------------------------------------------------------------------
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:    0.0470
   chunk 50 optimal weight:    0.7980
   chunk 65 optimal weight:    7.9990
   chunk 7 optimal weight:    0.2980
   chunk 4 optimal weight:    0.6980
   chunk 29 optimal weight:    0.1980
   chunk 80 optimal weight:    1.9990
   chunk 27 optimal weight:    0.3980
   chunk 14 optimal weight:    0.8980
   chunk 71 optimal weight:    0.5980
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.3078

-------------------------------------------------------------------------------
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 = 0.3887 r_free = 0.3887 target = 0.161963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.148419 restraints weight = 35528.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.149177 restraints weight = 33852.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.148118 restraints weight = 11331.660|
|-----------------------------------------------------------------------------|
r_work (final): 0.3701
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3701
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3701 r_free = 0.3701    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3701 r_free = 0.3701    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3701
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7429
moved from start:          0.3701

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= 0.182
  Angle     :  0.639   9.702   8989  Z= 0.311
  Chirality :  0.042   0.242   1070
  Planarity :  0.005   0.054   1105
  Dihedral  : 10.280 112.239   1430
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  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:  0.02 (0.29), residues: 862
  helix:  1.57 (0.27), residues: 379
  sheet: -0.07 (0.40), residues: 178
  loop : -1.98 (0.32), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.002   TRP A 112 
 HIS   0.001   0.000   HIS A 156 
 PHE   0.030   0.002   PHE A 431 
 TYR   0.023   0.002   TYR A 291 
 ARG   0.006   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
  120 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.611 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 LEU cc_start: 0.6288 (tp) cc_final: 0.5915 (tt)
REVERT: A  242 ILE cc_start: 0.8324 (mt) cc_final: 0.8112 (mm)
REVERT: A  315 PHE cc_start: 0.7719 (t80) cc_final: 0.7417 (t80)
REVERT: A  369 ILE cc_start: 0.8111 (mm) cc_final: 0.7856 (mm)
REVERT: B    7 PRO cc_start: 0.7481 (Cg_endo) cc_final: 0.7088 (Cg_exo)
REVERT: B   70 SER cc_start: 0.8471 (t) cc_final: 0.7903 (m)
REVERT: B   88 LEU cc_start: 0.7900 (pp) cc_final: 0.7313 (mp)
REVERT: C   81 ILE cc_start: 0.8047 (mm) cc_final: 0.7631 (mt)
REVERT: C  136 THR cc_start: 0.8660 (m) cc_final: 0.8309 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.1451
  time to fit residues: 24.4041
Evaluate side-chains
  101 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.556 
-------------------------------------------------------------------------------
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:    0.1980
   chunk 23 optimal weight:    0.1980
   chunk 42 optimal weight:    0.0770
   chunk 11 optimal weight:    0.9990
   chunk 75 optimal weight:    0.4980
   chunk 21 optimal weight:    0.8980
   chunk 7 optimal weight:    0.0570
   chunk 59 optimal weight:    0.0970
   chunk 17 optimal weight:    0.9980
   chunk 73 optimal weight:    5.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.1254

-------------------------------------------------------------------------------
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 = 0.3923 r_free = 0.3923 target = 0.165018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.152386 restraints weight = 32097.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.151411 restraints weight = 30028.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.149983 restraints weight = 12138.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.3718
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3718
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3718 r_free = 0.3718    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 = 0.3718 r_free = 0.3718    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
r_final: 0.3718
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7394
moved from start:          0.3807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   6564  Z= 0.154
  Angle     :  0.599   6.991   8989  Z= 0.295
  Chirality :  0.041   0.239   1070
  Planarity :  0.005   0.055   1105
  Dihedral  :  9.934 114.421   1430
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  0.19 %
    Favored  : 99.63 %
  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: 862
  helix:  1.63 (0.26), residues: 380
  sheet:  0.02 (0.40), residues: 176
  loop : -1.96 (0.32), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.002   TRP A 112 
 HIS   0.001   0.000   HIS A 156 
 PHE   0.028   0.001   PHE A 431 
 TYR   0.011   0.001   TYR A 489 
 ARG   0.006   0.000   ARG B 191 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2382.65 seconds
wall clock time: 42 minutes 16.18 seconds (2536.18 seconds total)