Starting phenix.real_space_refine
on Wed Mar 12 22:08:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d2w_27152/03_2025/8d2w_27152.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d2w_27152/03_2025/8d2w_27152.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8d2w_27152/03_2025/8d2w_27152.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d2w_27152/03_2025/8d2w_27152.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d2w_27152/03_2025/8d2w_27152.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d2w_27152/03_2025/8d2w_27152.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.045
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 1622 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: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      34      5.16       5
     C    4501      2.51       5
     N    1026      2.21       5
     O    1296      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6858
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3442
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 460, 3417
          Classifications: {'peptide': 460}
          Incomplete info: {'truncation_to_alanine': 49}
          Link IDs: {'PTRANS': 20, 'TRANS': 439}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 186
          Unresolved non-hydrogen angles: 224
          Unresolved non-hydrogen dihedrals: 157
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 115
      Conformer: "B"
        Number of residues, atoms: 460, 3417
          Classifications: {'peptide': 460}
          Incomplete info: {'truncation_to_alanine': 49}
          Link IDs: {'PTRANS': 20, 'TRANS': 439}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 186
          Unresolved non-hydrogen angles: 224
          Unresolved non-hydrogen dihedrals: 157
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 115
          bond proxies already assigned to first conformer: 3476
    Chain: "B"
      Number of atoms: 1404
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 201, 1393
          Classifications: {'peptide': 201}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 14, 'TRANS': 186}
          Unresolved non-hydrogen bonds: 60
          Unresolved non-hydrogen angles: 71
          Unresolved non-hydrogen dihedrals: 49
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 31
      Conformer: "B"
        Number of residues, atoms: 201, 1393
          Classifications: {'peptide': 201}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 14, 'TRANS': 186}
          Unresolved non-hydrogen bonds: 60
          Unresolved non-hydrogen angles: 71
          Unresolved non-hydrogen dihedrals: 49
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 31
          bond proxies already assigned to first conformer: 1419
    Chain: "C"
      Number of atoms: 1419
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 203, 1408
          Classifications: {'peptide': 203}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 12, 'TRANS': 190}
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 53
          Unresolved non-hydrogen dihedrals: 37
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 20
      Conformer: "B"
        Number of residues, atoms: 203, 1408
          Classifications: {'peptide': 203}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 12, 'TRANS': 190}
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 53
          Unresolved non-hydrogen dihedrals: 37
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 20
          bond proxies already assigned to first conformer: 1436
    Chain: "A"
      Number of atoms: 553
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 15, 448
          Unusual residues: {'LMT': 14, 'ZGS': 1}
          Classifications: {'undetermined': 15}
          Link IDs: {None: 14}
          Unresolved non-hydrogen bonds: 84
          Unresolved non-hydrogen angles: 126
          Unresolved non-hydrogen dihedrals: 179
          Unresolved non-hydrogen chiralities: 35
      Conformer: "B"
        Number of residues, atoms: 15, 448
          Unusual residues: {'LMT': 14, 'ZGS': 1}
          Classifications: {'undetermined': 15}
          Link IDs: {None: 14}
          Unresolved non-hydrogen bonds: 84
          Unresolved non-hydrogen angles: 126
          Unresolved non-hydrogen dihedrals: 179
          Unresolved non-hydrogen chiralities: 35
          bond proxies already assigned to first conformer: 346
    Chain: "C"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 35
          Unusual residues: {'LMT': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 5
          Classifications: {'water': 5}
          Link IDs: {None: 4}
  Residues with excluded nonbonded symmetry interactions: 7
    residue:
      pdb=" N  ATRP A 346 " occ=0.50
      ... (26 atoms not shown)
      pdb=" CH2BTRP A 346 " occ=0.50
    residue:
      pdb=" N  APHE A 449 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE A 449 " occ=0.50
    residue:
      pdb=" N  AARG B 191 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG B 191 " occ=0.50
    residue:
      pdb=" N  AARG C  13 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG C  13 " occ=0.50
    residue:
      pdb=" C1 ALMT A 602 " occ=0.50
      ... (68 atoms not shown)
      pdb=" O6BBLMT A 602 " occ=0.50
    residue:
      pdb=" C1 ALMT A 603 " occ=0.50
      ... (68 atoms not shown)
      pdb=" O6BBLMT A 603 " occ=0.50
    residue:
      pdb=" C1 ALMT A 610 " occ=0.50
      ... (68 atoms not shown)
      pdb=" O6BBLMT A 610 " occ=0.50
  Time building chain proxies: 8.43, per 1000 atoms: 1.23
  Number of scatterers: 6858
  At special positions: 0
  Unit cell: (69.208, 73.428, 141.792, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      34     16.00
     P       1     15.00
     O    1296      8.00
     N    1026      7.00
     C    4501      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: 1.97
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1572

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 10 sheets defined
      45.5% alpha, 17.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.94
  Creating SS restraints...
    Processing helix  chain 'A' and resid 36 through 46
    Processing helix  chain 'A' and resid 47 through 67
      removed outlier: 3.998A  pdb=" N   GLN A  51 " --> pdb=" O   GLY A  47 " (cutoff:3.500A)
      removed outlier: 6.143A  pdb=" N   GLN A  62 " --> pdb=" O   GLY A  58 " (cutoff:3.500A)
      removed outlier: 5.286A  pdb=" N   ILE A  63 " --> pdb=" O   PHE A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 100
      removed outlier: 4.021A  pdb=" N   ALA A  88 " --> pdb=" O   ARG A  84 " (cutoff:3.500A)
      Proline residue:  A  92  - end of helix
    Processing helix  chain 'A' and resid 109 through 128
      Proline residue:  A 118  - end of helix
      removed outlier: 3.715A  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 163 through 165
      No H-bonds generated for 'chain 'A' and resid 163 through 165'
    Processing helix  chain 'A' and resid 169 through 200
    Processing helix  chain 'A' and resid 232 through 262
      removed outlier: 3.512A  pdb=" N   VAL A 262 " --> pdb=" O   LEU A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 288
    Processing helix  chain 'A' and resid 288 through 311
    Processing helix  chain 'A' and resid 312 through 319
    Processing helix  chain 'A' and resid 325 through 352
      Proline residue:  A 342  - end of helix
      removed outlier: 3.770A  pdb=" N   THR A 349 " --> pdb=" O   GLN A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 371
      removed outlier: 3.664A  pdb=" N   THR A 361 " --> pdb=" O   VAL A 357 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   VAL A 364 " --> pdb=" O   GLY A 360 " (cutoff:3.500A)
      removed outlier: 4.550A  pdb=" N   VAL A 365 " --> pdb=" O   THR A 361 " (cutoff:3.500A)
      Proline residue:  A 366  - end of helix
    Processing helix  chain 'A' and resid 377 through 414
      removed outlier: 3.535A  pdb=" N   TYR A 382 " --> pdb=" O   LEU A 378 " (cutoff:3.500A)
      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: 3.542A  pdb=" N   TYR A 425 " --> pdb=" O   GLU A 421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 473
      removed outlier: 3.574A  pdb=" N   LEU A 465 " --> pdb=" O   GLY A 461 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 488
      removed outlier: 3.570A  pdb=" N   SER A 488 " --> pdb=" O   LEU A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 493 through 507
      removed outlier: 3.644A  pdb=" N   GLN A 497 " --> pdb=" O   GLU A 493 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   GLY A 498 " --> pdb=" O   GLU A 494 " (cutoff:3.500A)
      removed outlier: 5.522A  pdb=" N   ASN A 499 " --> pdb=" O   LYS A 495 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 123
    Processing helix  chain 'C' and resid 28 through 31
    Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 5
    Processing sheet with id=AA2, first strand: chain 'B' and resid 11 through 12
      removed outlier: 5.976A  pdb=" N   LYS B  11 " --> pdb=" O   ASN B 102 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   VAL B  32 " --> pdb=" O   TYR B  48 " (cutoff:3.500A)
      removed outlier: 4.582A  pdb=" N   TYR B  48 " --> pdb=" O   VAL B  32 " (cutoff:3.500A)
      removed outlier: 6.405A  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: 4.858A  pdb=" N   ALA B 127 " --> pdb=" O   ILE B 174 " (cutoff:3.500A)
      removed outlier: 7.185A  pdb=" N   ILE B 174 " --> pdb=" O   ALA B 127 " (cutoff:3.500A)
      removed outlier: 5.666A  pdb=" N   VAL B 129 " --> pdb=" O   LEU B 172 " (cutoff:3.500A)
      removed outlier: 7.304A  pdb=" N   LEU B 172 " --> pdb=" O   VAL B 129 " (cutoff:3.500A)
      removed outlier: 5.534A  pdb=" N   PHE B 131 " --> pdb=" O   ALA B 170 " (cutoff:3.500A)
      removed outlier: 7.166A  pdb=" N   ALA B 170 " --> pdb=" O   PHE B 131 " (cutoff:3.500A)
      removed outlier: 5.434A  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: 4.658A  pdb=" N   TRP B 143 " --> pdb=" O   GLN B 149 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 3 through 6
      removed outlier: 3.646A  pdb=" N   GLU C   5 " --> pdb=" O   LYS C  23 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 33 through 35
    Processing sheet with id=AA7, first strand: chain 'C' and resid 89 through 91
    Processing sheet with id=AA8, first strand: chain 'C' and resid 121 through 123
      removed outlier: 5.886A  pdb=" N   TRP C 170 " --> pdb=" O   GLY C 143 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 121 through 123
      removed outlier: 5.886A  pdb=" N   TRP C 170 " --> pdb=" O   GLY C 143 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   LEU C 169 " --> pdb=" O   ASN C 166 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 185 through 187

    384 hydrogen bonds defined for protein.
    1088 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.67

  Time building geometry restraints manager: 2.30 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 990
        1.30 -     1.43: 1870
        1.43 -     1.56: 4019
        1.56 -     1.68: 110
        1.68 -     1.81: 48
  Bond restraints: 7037
  Sorted by residual:
  bond pdb=" C1BALMT A 603 "
       pdb=" O5BALMT A 603 "
    ideal  model  delta    sigma   weight residual
    1.393  1.519 -0.126 2.00e-02 2.50e+03 3.98e+01
  bond pdb=" C1B LMT A 604 "
       pdb=" O5B LMT A 604 "
    ideal  model  delta    sigma   weight residual
    1.393  1.517 -0.124 2.00e-02 2.50e+03 3.82e+01
  bond pdb=" C1BBLMT A 602 "
       pdb=" O5BBLMT A 602 "
    ideal  model  delta    sigma   weight residual
    1.393  1.514 -0.121 2.00e-02 2.50e+03 3.67e+01
  bond pdb=" C1B LMT A 611 "
       pdb=" O5B LMT A 611 "
    ideal  model  delta    sigma   weight residual
    1.393  1.513 -0.120 2.00e-02 2.50e+03 3.62e+01
  bond pdb=" C1B LMT A 605 "
       pdb=" O5B LMT A 605 "
    ideal  model  delta    sigma   weight residual
    1.393  1.513 -0.120 2.00e-02 2.50e+03 3.61e+01
  ... (remaining 7032 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.95: 9361
        4.95 -     9.89: 212
        9.89 -    14.84: 3
       14.84 -    19.79: 3
       19.79 -    24.74: 3
  Bond angle restraints: 9582
  Sorted by residual:
  angle pdb=" C03 ZGS A 601 "
        pdb=" C04 ZGS A 601 "
        pdb=" C05 ZGS A 601 "
      ideal   model   delta    sigma   weight residual
     127.34  152.08  -24.74 3.00e+00 1.11e-01 6.80e+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  151.03  -23.87 3.00e+00 1.11e-01 6.33e+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  151.32  -23.80 3.00e+00 1.11e-01 6.29e+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  129.66  -18.96 3.00e+00 1.11e-01 3.99e+01
  angle pdb=" C02 ZGS A 601 "
        pdb=" C03 ZGS A 601 "
        pdb=" C04 ZGS A 601 "
      ideal   model   delta    sigma   weight residual
     127.67  111.44   16.23 3.00e+00 1.11e-01 2.93e+01
  ... (remaining 9577 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.54: 4151
       29.54 -    59.08: 248
       59.08 -    88.62: 93
       88.62 -   118.15: 137
      118.15 -   147.69: 5
  Dihedral angle restraints: 4634
    sinusoidal: 2166
      harmonic: 2468
  Sorted by residual:
  dihedral pdb=" C23 ZGS A 601 "
           pdb=" O24 ZGS A 601 "
           pdb=" P25 ZGS A 601 "
           pdb=" O26 ZGS A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     177.58  -34.73 -147.69     1      3.00e+01 1.11e-03 1.97e+01
  dihedral pdb=" C5B LMT C 301 "
           pdb=" C1B LMT C 301 "
           pdb=" O5B LMT C 301 "
           pdb=" O1B LMT C 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
     295.61  173.64  121.97     1      3.00e+01 1.11e-03 1.63e+01
  dihedral pdb=" C2B LMT C 301 "
           pdb=" C1B LMT C 301 "
           pdb=" O5B LMT C 301 "
           pdb=" C5B LMT C 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -57.12   64.84 -121.96     1      3.00e+01 1.11e-03 1.63e+01
  ... (remaining 4631 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 849
       0.050 -    0.100: 225
       0.100 -    0.150: 68
       0.150 -    0.200: 9
       0.200 -    0.250: 5
  Chirality restraints: 1156
  Sorted by residual:
  chirality pdb=" C1BALMT A 602 "
            pdb=" C2BALMT A 602 "
            pdb=" O1BALMT A 602 "
            pdb=" O5BALMT A 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.20   -2.45    0.25 2.00e-01 2.50e+01 1.56e+00
  chirality pdb=" 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   -2.43    0.23 2.00e-01 2.50e+01 1.31e+00
  chirality pdb=" C1B LMT A 608 "
            pdb=" C2B LMT A 608 "
            pdb=" O1B LMT A 608 "
            pdb=" O5B LMT A 608 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.20   -2.42    0.22 2.00e-01 2.50e+01 1.18e+00
  ... (remaining 1153 not shown)

  Planarity restraints: 1130
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP C  46 "   -0.038 5.00e-02 4.00e+02   5.84e-02 5.46e+00
        pdb=" N   PRO C  47 "    0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO C  47 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO C  47 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B  75 "   -0.033 5.00e-02 4.00e+02   4.97e-02 3.96e+00
        pdb=" N   PRO B  76 "    0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO B  76 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B  76 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 374 "    0.030 5.00e-02 4.00e+02   4.51e-02 3.26e+00
        pdb=" N   PRO A 375 "   -0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO A 375 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 375 "    0.025 5.00e-02 4.00e+02
  ... (remaining 1127 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 1748
        2.80 -     3.33: 6113
        3.33 -     3.85: 11558
        3.85 -     4.38: 12697
        4.38 -     4.90: 22836
  Nonbonded interactions: 54952
  Sorted by model distance:
  nonbonded pdb=" O   TYR A  43 "
            pdb=" OH  TYR A 159 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" OD1 ASP A  67 "
            pdb=" OH  TYR A 452 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" OH  TYR A 425 "
            pdb=" O   HOH A 701 "
     model   vdw
     2.314 3.040
  nonbonded pdb=" O   TYR A 452 "
            pdb=" ND2 ASN C  99 "
     model   vdw
     2.322 3.120
  nonbonded pdb=" O3' LMT A 607 "
            pdb=" O6'BLMT A 610 "
     model   vdw
     2.329 3.040
  ... (remaining 54947 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=0.98
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.240
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  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:                     25.650
  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:3.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
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      :  0.012   0.126   7037  Z= 0.765
  Angle     :  1.387  24.737   9582  Z= 0.547
  Chirality :  0.053   0.250   1156
  Planarity :  0.006   0.058   1130
  Dihedral  : 29.930 147.692   3050
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.54 %
    Favored  : 93.34 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  :  7.55 %
    Favored  : 91.61 %
  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: -1.42 (0.27), residues: 868
  helix:  0.47 (0.24), residues: 385
  sheet: -0.76 (0.43), residues: 150
  loop : -2.76 (0.30), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C  33 
 HIS   0.001   0.000   HIS A 156 
 PHE   0.025   0.002   PHE B  89 
 TYR   0.013   0.001   TYR A 251 
 ARG   0.002   0.000   ARG C  40 

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 132
  time to evaluate  : 1.034 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 ARG cc_start: 0.7242 (mmm-85) cc_final: 0.6932 (ttm-80)
REVERT: A  159 TYR cc_start: 0.8602 (t80) cc_final: 0.8345 (t80)
REVERT: A  173 ARG cc_start: 0.7234 (mtt180) cc_final: 0.6781 (mtt-85)
REVERT: A  199 VAL cc_start: 0.8805 (t) cc_final: 0.8386 (m)
REVERT: A  288 HIS cc_start: 0.7354 (t-90) cc_final: 0.6738 (t-90)
REVERT: A  296 MET cc_start: 0.6886 (mmt) cc_final: 0.6637 (mmp)
REVERT: A  413 GLN cc_start: 0.8528 (mm110) cc_final: 0.8012 (mt0)
  outliers start: 5
  outliers final: 0
  residues processed: 135
  average time/residue: 0.2044
  time to fit residues: 36.6531
Evaluate side-chains
  97 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 22 optimal weight:    5.9990
   chunk 43 optimal weight:    0.6980
   chunk 34 optimal weight:    0.5980
   chunk 67 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9990
   chunk 50 optimal weight:    0.2980
   chunk 78 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 149 GLN
A 152 GLN
A 319 ASN
A 413 GLN
B 190 ASN
C  74 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.170508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.136682 restraints weight = 37604.942|
|-----------------------------------------------------------------------------|
r_work (start): 0.3588 rms_B_bonded: 6.41
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3589
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3589 r_free = 0.3589    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3589 r_free = 0.3589    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3589
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.1771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.080   7037  Z= 0.302
  Angle     :  0.894   9.925   9582  Z= 0.382
  Chirality :  0.052   0.304   1156
  Planarity :  0.005   0.057   1130
  Dihedral  : 19.396 156.216   1869
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.43 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 14.60 %
    Favored  : 83.22 %
  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: -0.82 (0.28), residues: 868
  helix:  1.38 (0.25), residues: 381
  sheet: -1.12 (0.41), residues: 175
  loop : -2.72 (0.31), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 140 
 HIS   0.002   0.001   HIS A 156 
 PHE   0.024   0.002   PHE A 367 
 TYR   0.013   0.002   TYR A 291 
 ARG   0.005   0.001   ARG B 104 

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 102
  time to evaluate  : 0.686 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 ARG cc_start: 0.7871 (mmm-85) cc_final: 0.7533 (ttm-80)
REVERT: A  164 MET cc_start: 0.8260 (mmt) cc_final: 0.7999 (mmm)
REVERT: A  172 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7942 (mt-10)
REVERT: B  110 GLN cc_start: 0.7175 (tt0) cc_final: 0.6916 (mt0)
REVERT: B  196 PHE cc_start: 0.8023 (m-80) cc_final: 0.7745 (m-80)
  outliers start: 13
  outliers final: 8
  residues processed: 110
  average time/residue: 0.2095
  time to fit residues: 31.5149
Evaluate side-chains
  106 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 98
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 ASN
Chi-restraints excluded: chain A residue  359 ILE
Chi-restraints excluded: chain A residue  439 SER
Chi-restraints excluded: chain B residue    4 ILE
Chi-restraints excluded: chain B residue    5 ASN
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain C residue  151 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 54 optimal weight:    0.7980
   chunk 23 optimal weight:    6.9990
   chunk 77 optimal weight:    0.6980
   chunk 50 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 73 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 16 optimal weight:    0.6980
   chunk 46 optimal weight:    2.9990
   chunk 3 optimal weight:    0.5980
   chunk 33 optimal weight:    0.6980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3965 r_free = 0.3965 target = 0.169673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.135218 restraints weight = 38160.362|
|-----------------------------------------------------------------------------|
r_work (start): 0.3571 rms_B_bonded: 6.56
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3573
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3573 r_free = 0.3573    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3573 r_free = 0.3573    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3573
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.2046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   7037  Z= 0.269
  Angle     :  0.743   9.617   9582  Z= 0.337
  Chirality :  0.045   0.325   1156
  Planarity :  0.005   0.056   1130
  Dihedral  : 14.289 150.947   1869
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.19 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 15.10 %
    Favored  : 82.21 %
  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: -0.63 (0.29), residues: 868
  helix:  1.65 (0.26), residues: 379
  sheet: -1.16 (0.41), residues: 175
  loop : -2.65 (0.31), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  95 
 HIS   0.002   0.001   HIS A 156 
 PHE   0.022   0.002   PHE B  89 
 TYR   0.012   0.001   TYR A 291 
 ARG   0.004   0.001   ARG B 104 

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 0.667 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 ARG cc_start: 0.7841 (mmm-85) cc_final: 0.7463 (ttm-80)
REVERT: A  173 ARG cc_start: 0.7279 (mtt180) cc_final: 0.7059 (mtt-85)
REVERT: A  288 HIS cc_start: 0.6439 (t-170) cc_final: 0.5147 (t-170)
REVERT: A  291 TYR cc_start: 0.6743 (OUTLIER) cc_final: 0.6400 (t80)
REVERT: A  296 MET cc_start: 0.7467 (OUTLIER) cc_final: 0.6614 (tpp)
REVERT: A  319 ASN cc_start: 0.8126 (OUTLIER) cc_final: 0.7718 (m-40)
REVERT: B  110 GLN cc_start: 0.7156 (tt0) cc_final: 0.6927 (mt0)
REVERT: B  196 PHE cc_start: 0.8045 (m-80) cc_final: 0.7737 (m-80)
  outliers start: 16
  outliers final: 7
  residues processed: 108
  average time/residue: 0.2392
  time to fit residues: 34.9456
Evaluate side-chains
  107 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.868 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  296 MET
Chi-restraints excluded: chain A residue  319 ASN
Chi-restraints excluded: chain A residue  439 SER
Chi-restraints excluded: chain A residue  440 LEU
Chi-restraints excluded: chain A residue  480 ILE
Chi-restraints excluded: chain A residue  484 LEU
Chi-restraints excluded: chain B residue    5 ASN
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  112 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 15 optimal weight:    0.6980
   chunk 65 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 69 optimal weight:    0.7980
   chunk 79 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9990
   chunk 68 optimal weight:    0.8980
   chunk 53 optimal weight:    0.0770
   chunk 70 optimal weight:    0.6980
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
A 319 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.169691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.135294 restraints weight = 34388.427|
|-----------------------------------------------------------------------------|
r_work (start): 0.3569 rms_B_bonded: 6.10
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3571
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3571 r_free = 0.3571    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3571 r_free = 0.3571    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3571
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.2253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   7037  Z= 0.247
  Angle     :  0.686  10.327   9582  Z= 0.317
  Chirality :  0.042   0.294   1156
  Planarity :  0.005   0.055   1130
  Dihedral  : 12.643 148.408   1869
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.31 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 15.94 %
    Favored  : 82.38 %
  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: -0.47 (0.29), residues: 868
  helix:  1.81 (0.26), residues: 379
  sheet: -1.14 (0.42), residues: 173
  loop : -2.55 (0.32), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C  95 
 HIS   0.002   0.001   HIS A 288 
 PHE   0.026   0.002   PHE A 367 
 TYR   0.012   0.001   TYR A 358 
 ARG   0.004   0.001   ARG B 104 

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 98
  time to evaluate  : 1.145 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 ARG cc_start: 0.7780 (mmm-85) cc_final: 0.7356 (ttm-80)
REVERT: A  296 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.6418 (tpp)
REVERT: B  196 PHE cc_start: 0.7964 (m-80) cc_final: 0.7713 (m-80)
  outliers start: 10
  outliers final: 6
  residues processed: 102
  average time/residue: 0.2340
  time to fit residues: 32.6870
Evaluate side-chains
  102 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 0.642 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  296 MET
Chi-restraints excluded: chain A residue  480 ILE
Chi-restraints excluded: chain A residue  484 LEU
Chi-restraints excluded: chain B residue    5 ASN
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  141 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 49 optimal weight:    0.6980
   chunk 67 optimal weight:    0.4980
   chunk 50 optimal weight:    0.8980
   chunk 27 optimal weight:    0.4980
   chunk 29 optimal weight:    0.8980
   chunk 10 optimal weight:    0.6980
   chunk 65 optimal weight:    0.0060
   chunk 2 optimal weight:    0.7980
   chunk 18 optimal weight:    0.8980
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.4796

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

Flipped N/Q/H residues before XYZ refinement:
A 319 ASN
** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.170350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.138088 restraints weight = 39589.827|
|-----------------------------------------------------------------------------|
r_work (start): 0.3612 rms_B_bonded: 5.94
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3607
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3607 r_free = 0.3607    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3607 r_free = 0.3607    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3607
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.2443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   7037  Z= 0.216
  Angle     :  0.663  10.374   9582  Z= 0.306
  Chirality :  0.041   0.290   1156
  Planarity :  0.005   0.051   1130
  Dihedral  : 12.021 149.613   1869
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.49 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 16.44 %
    Favored  : 82.05 %
  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: -0.33 (0.29), residues: 868
  helix:  1.95 (0.26), residues: 379
  sheet: -1.09 (0.41), residues: 174
  loop : -2.52 (0.32), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 103 
 HIS   0.002   0.001   HIS A 288 
 PHE   0.019   0.001   PHE B  89 
 TYR   0.010   0.001   TYR B  48 
 ARG   0.009   0.001   ARG A 173 

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.693 
Fit side-chains
REVERT: A  100 ARG cc_start: 0.7882 (mmm-85) cc_final: 0.7454 (ttm-80)
REVERT: A  291 TYR cc_start: 0.6777 (OUTLIER) cc_final: 0.6328 (t80)
REVERT: A  296 MET cc_start: 0.7298 (OUTLIER) cc_final: 0.6331 (tpp)
  outliers start: 9
  outliers final: 6
  residues processed: 100
  average time/residue: 0.1944
  time to fit residues: 25.9736
Evaluate side-chains
  103 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 GLU
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  296 MET
Chi-restraints excluded: chain A residue  439 SER
Chi-restraints excluded: chain A residue  480 ILE
Chi-restraints excluded: chain B residue    5 ASN
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  141 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   chunk 59 optimal weight:    0.6980
   chunk 72 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   chunk 44 optimal weight:    4.9990
   chunk 70 optimal weight:    0.4980
   chunk 13 optimal weight:    2.9990
   chunk 41 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 319 ASN
** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.168938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.145221 restraints weight = 36129.213|
|-----------------------------------------------------------------------------|
r_work (start): 0.3678 rms_B_bonded: 3.53
r_work (final): 0.3678
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3688
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3688 r_free = 0.3688    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3688 r_free = 0.3688    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3688
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.2556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   7037  Z= 0.256
  Angle     :  0.680  10.170   9582  Z= 0.315
  Chirality :  0.042   0.292   1156
  Planarity :  0.005   0.052   1130
  Dihedral  : 11.792 151.089   1869
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.19 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 15.94 %
    Favored  : 82.38 %
  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: -0.38 (0.29), residues: 868
  helix:  1.79 (0.26), residues: 386
  sheet: -1.18 (0.41), residues: 173
  loop : -2.42 (0.32), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP A 103 
 HIS   0.002   0.001   HIS A 156 
 PHE   0.028   0.002   PHE A 367 
 TYR   0.011   0.001   TYR A 358 
 ARG   0.002   0.000   ARG A  34 

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.603 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 ARG cc_start: 0.7538 (mmm-85) cc_final: 0.7175 (ttm-80)
REVERT: A  291 TYR cc_start: 0.6619 (OUTLIER) cc_final: 0.6345 (t80)
REVERT: A  296 MET cc_start: 0.6968 (OUTLIER) cc_final: 0.6055 (tpp)
  outliers start: 10
  outliers final: 5
  residues processed: 101
  average time/residue: 0.1981
  time to fit residues: 27.1801
Evaluate side-chains
  102 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 0.826 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  296 MET
Chi-restraints excluded: chain A residue  439 SER
Chi-restraints excluded: chain A residue  480 ILE
Chi-restraints excluded: chain B residue    5 ASN
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  141 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 35 optimal weight:    0.2980
   chunk 27 optimal weight:    0.6980
   chunk 51 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 52 optimal weight:    0.7980
   chunk 6 optimal weight:    0.3980
   chunk 70 optimal weight:    0.0970
   chunk 45 optimal weight:   30.0000
   overall best weight:    0.4578

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

Flipped N/Q/H residues before XYZ refinement:
A 319 ASN
** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.171384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.141953 restraints weight = 40213.900|
|-----------------------------------------------------------------------------|
r_work (start): 0.3576 rms_B_bonded: 6.45
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3576
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3576 r_free = 0.3576    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3576 r_free = 0.3576    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3576
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.2679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   7037  Z= 0.206
  Angle     :  0.646  10.440   9582  Z= 0.300
  Chirality :  0.040   0.284   1156
  Planarity :  0.005   0.053   1130
  Dihedral  : 11.393 152.255   1869
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.37 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 16.61 %
    Favored  : 81.71 %
  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: -0.25 (0.29), residues: 868
  helix:  1.91 (0.26), residues: 386
  sheet: -1.14 (0.41), residues: 169
  loop : -2.33 (0.32), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP A 103 
 HIS   0.002   0.001   HIS A 156 
 PHE   0.017   0.001   PHE B  89 
 TYR   0.010   0.001   TYR B  48 
 ARG   0.004   0.000   ARG A 173 

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 98
  time to evaluate  : 0.681 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 ARG cc_start: 0.8054 (mmm-85) cc_final: 0.7653 (ttm-80)
REVERT: A  291 TYR cc_start: 0.6610 (OUTLIER) cc_final: 0.6258 (t80)
REVERT: A  296 MET cc_start: 0.7361 (OUTLIER) cc_final: 0.6485 (tpp)
REVERT: A  354 LYS cc_start: 0.7599 (ttpp) cc_final: 0.7233 (ttmt)
  outliers start: 10
  outliers final: 6
  residues processed: 102
  average time/residue: 0.1948
  time to fit residues: 26.6377
Evaluate side-chains
  101 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 0.661 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ARG
Chi-restraints excluded: chain A residue  210 GLU
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  296 MET
Chi-restraints excluded: chain A residue  439 SER
Chi-restraints excluded: chain B residue    5 ASN
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  141 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 75 optimal weight:    0.2980
   chunk 81 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 68 optimal weight:    0.8980
   chunk 34 optimal weight:    0.6980
   chunk 47 optimal weight:    0.3980
   chunk 8 optimal weight:    0.6980
   chunk 4 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9980
   chunk 67 optimal weight:    0.0870
   overall best weight:    0.3958

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

Flipped N/Q/H residues before XYZ refinement:
A 319 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.171967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.143690 restraints weight = 34435.337|
|-----------------------------------------------------------------------------|
r_work (start): 0.3614 rms_B_bonded: 5.54
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3614
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3614 r_free = 0.3614    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3614 r_free = 0.3614    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3614
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.2732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7037  Z= 0.193
  Angle     :  0.639  10.583   9582  Z= 0.296
  Chirality :  0.040   0.281   1156
  Planarity :  0.005   0.053   1130
  Dihedral  : 11.081 153.716   1869
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.49 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 16.95 %
    Favored  : 81.38 %
  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: -0.18 (0.29), residues: 868
  helix:  1.95 (0.26), residues: 387
  sheet: -1.12 (0.41), residues: 169
  loop : -2.28 (0.33), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 103 
 HIS   0.004   0.002   HIS A 288 
 PHE   0.018   0.001   PHE A 367 
 TYR   0.009   0.001   TYR B  48 
 ARG   0.007   0.000   ARG A 173 

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.622 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 ARG cc_start: 0.8041 (mmm-85) cc_final: 0.7592 (ttm-80)
REVERT: A  291 TYR cc_start: 0.6757 (OUTLIER) cc_final: 0.6353 (t80)
REVERT: A  296 MET cc_start: 0.7244 (OUTLIER) cc_final: 0.6349 (tpp)
REVERT: A  354 LYS cc_start: 0.7548 (ttpp) cc_final: 0.7155 (ttmt)
  outliers start: 10
  outliers final: 6
  residues processed: 99
  average time/residue: 0.1917
  time to fit residues: 25.2159
Evaluate side-chains
  104 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 96
  time to evaluate  : 0.600 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 GLU
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  296 MET
Chi-restraints excluded: chain A residue  439 SER
Chi-restraints excluded: chain B residue    5 ASN
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  141 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 69 optimal weight:    0.3980
   chunk 51 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 78 optimal weight:    0.0020
   chunk 82 optimal weight:    0.0970
   chunk 48 optimal weight:    0.1980
   chunk 32 optimal weight:    1.9990
   chunk 42 optimal weight:    0.6980
   chunk 81 optimal weight:    0.7980
   chunk 47 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9980
   overall best weight:    0.2786

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

Flipped N/Q/H residues before XYZ refinement:
A 319 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.173528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.146896 restraints weight = 33896.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.3660 rms_B_bonded: 5.08
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3660
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3660 r_free = 0.3660    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3660 r_free = 0.3660    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3660
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.2848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7037  Z= 0.166
  Angle     :  0.622  10.839   9582  Z= 0.289
  Chirality :  0.040   0.275   1156
  Planarity :  0.005   0.054   1130
  Dihedral  : 10.784 155.243   1869
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.67 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 17.95 %
    Favored  : 80.87 %
  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: -0.09 (0.29), residues: 868
  helix:  2.04 (0.26), residues: 387
  sheet: -1.11 (0.41), residues: 169
  loop : -2.24 (0.33), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP A 103 
 HIS   0.005   0.002   HIS A 288 
 PHE   0.014   0.001   PHE B  89 
 TYR   0.009   0.001   TYR B  48 
 ARG   0.006   0.000   ARG A 173 

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 97
  time to evaluate  : 0.619 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 ARG cc_start: 0.7994 (mmm-85) cc_final: 0.7554 (ttm-80)
REVERT: A  291 TYR cc_start: 0.6616 (OUTLIER) cc_final: 0.6268 (t80)
REVERT: A  296 MET cc_start: 0.7128 (OUTLIER) cc_final: 0.6260 (tpp)
REVERT: A  354 LYS cc_start: 0.7467 (ttpp) cc_final: 0.7091 (ttmt)
  outliers start: 7
  outliers final: 4
  residues processed: 100
  average time/residue: 0.1943
  time to fit residues: 25.9187
Evaluate side-chains
  101 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 95
  time to evaluate  : 0.613 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 GLU
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  296 MET
Chi-restraints excluded: chain A residue  439 SER
Chi-restraints excluded: chain B residue    5 ASN
Chi-restraints excluded: chain B residue  141 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 80 optimal weight:    0.8980
   chunk 45 optimal weight:    7.9990
   chunk 31 optimal weight:    0.8980
   chunk 64 optimal weight:    6.9990
   chunk 59 optimal weight:    0.0070
   chunk 84 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9990
   chunk 12 optimal weight:    0.6980
   chunk 77 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.6998

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

Flipped N/Q/H residues before XYZ refinement:
A 319 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.169109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.144517 restraints weight = 27579.358|
|-----------------------------------------------------------------------------|
r_work (start): 0.3656 rms_B_bonded: 3.82
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3657
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3657 r_free = 0.3657    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3657 r_free = 0.3657    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3657
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.2867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   7037  Z= 0.266
  Angle     :  0.679  10.495   9582  Z= 0.315
  Chirality :  0.042   0.287   1156
  Planarity :  0.005   0.055   1130
  Dihedral  : 10.905 155.547   1869
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.31 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 18.46 %
    Favored  : 80.20 %
  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: -0.22 (0.29), residues: 868
  helix:  1.96 (0.26), residues: 383
  sheet: -1.13 (0.42), residues: 169
  loop : -2.32 (0.33), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP A 103 
 HIS   0.005   0.002   HIS A 288 
 PHE   0.032   0.002   PHE A 367 
 TYR   0.011   0.001   TYR B  48 
 ARG   0.008   0.001   ARG A 173 

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 96
  time to evaluate  : 0.824 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 ARG cc_start: 0.7855 (mmm-85) cc_final: 0.7432 (ttm-80)
REVERT: A  291 TYR cc_start: 0.6877 (OUTLIER) cc_final: 0.6507 (t80)
REVERT: A  296 MET cc_start: 0.7126 (OUTLIER) cc_final: 0.6233 (tpp)
REVERT: A  354 LYS cc_start: 0.7348 (ttpp) cc_final: 0.7007 (ttmt)
  outliers start: 8
  outliers final: 5
  residues processed: 98
  average time/residue: 0.2533
  time to fit residues: 33.1858
Evaluate side-chains
  102 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ARG
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  296 MET
Chi-restraints excluded: chain A residue  439 SER
Chi-restraints excluded: chain B residue    4 ILE
Chi-restraints excluded: chain B residue    5 ASN
Chi-restraints excluded: chain B residue  141 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 4 optimal weight:    0.5980
   chunk 66 optimal weight:    0.0050
   chunk 31 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 85 optimal weight:    0.0050
   chunk 59 optimal weight:    0.0980
   chunk 63 optimal weight:    3.9990
   chunk 8 optimal weight:    0.8980
   chunk 73 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9980
   chunk 21 optimal weight:    0.0070
   overall best weight:    0.1426

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

Flipped N/Q/H residues before XYZ refinement:
A 319 ASN
B  36 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.173696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.142160 restraints weight = 35913.684|
|-----------------------------------------------------------------------------|
r_work (start): 0.3664 rms_B_bonded: 5.81
r_work (final): 0.3664
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3664
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3664 r_free = 0.3664    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3664 r_free = 0.3664    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3664
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.2994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   7037  Z= 0.148
  Angle     :  0.622  10.713   9582  Z= 0.288
  Chirality :  0.039   0.268   1156
  Planarity :  0.005   0.055   1130
  Dihedral  : 10.453 157.557   1869
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.02 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 18.79 %
    Favored  : 80.03 %
  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:  0.03 (0.30), residues: 868
  helix:  2.11 (0.26), residues: 387
  sheet: -0.94 (0.41), residues: 169
  loop : -2.19 (0.34), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 103 
 HIS   0.005   0.002   HIS A 288 
 PHE   0.011   0.001   PHE B  89 
 TYR   0.009   0.001   TYR B  48 
 ARG   0.005   0.000   ARG A 173 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3692.18 seconds
wall clock time: 67 minutes 50.29 seconds (4070.29 seconds total)