Starting phenix.real_space_refine
on Sat Jul 26 04:23:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d2u_27150/07_2025/8d2u_27150.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d2u_27150/07_2025/8d2u_27150.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8d2u_27150/07_2025/8d2u_27150.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d2u_27150/07_2025/8d2u_27150.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d2u_27150/07_2025/8d2u_27150.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d2u_27150/07_2025/8d2u_27150.cif"
  }
  resolution = 3.3
  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=   0.050
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 1613 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      38      5.16       5
     Na      1      4.78       5
     C    4504      2.51       5
     N    1023      2.21       5
     O    1295      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6862
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 3465
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 460, 3431
          Classifications: {'peptide': 460}
          Incomplete info: {'truncation_to_alanine': 43}
          Link IDs: {'PTRANS': 20, 'TRANS': 439}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 169
          Unresolved non-hydrogen angles: 206
          Unresolved non-hydrogen dihedrals: 137
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 8}
          Unresolved non-hydrogen planarities: 112
      Conformer: "B"
        Number of residues, atoms: 460, 3431
          Classifications: {'peptide': 460}
          Incomplete info: {'truncation_to_alanine': 43}
          Link IDs: {'PTRANS': 20, 'TRANS': 439}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 169
          Unresolved non-hydrogen angles: 206
          Unresolved non-hydrogen dihedrals: 137
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 8}
          Unresolved non-hydrogen planarities: 112
          bond proxies already assigned to first conformer: 3483
    Chain: "B"
      Number of atoms: 1411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1411
          Classifications: {'peptide': 201}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 14, 'TRANS': 186}
          Unresolved non-hydrogen bonds: 42
          Unresolved non-hydrogen angles: 51
          Unresolved non-hydrogen dihedrals: 33
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 27
    Chain: "C"
      Number of atoms: 1415
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 203, 1415
          Classifications: {'peptide': 203}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 12, 'TRANS': 190}
          Unresolved non-hydrogen bonds: 38
          Unresolved non-hydrogen angles: 46
          Unresolved non-hydrogen dihedrals: 30
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 14
    Chain: "A"
      Number of atoms: 531
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 17, 472
          Unusual residues: {' NA': 1, 'LMT': 15, 'ZGS': 1}
          Classifications: {'undetermined': 17}
          Link IDs: {None: 16}
          Unresolved non-hydrogen bonds: 97
          Unresolved non-hydrogen angles: 146
          Unresolved non-hydrogen dihedrals: 210
          Unresolved non-hydrogen chiralities: 41
      Conformer: "B"
        Number of residues, atoms: 17, 472
          Unusual residues: {' NA': 1, 'LMT': 15, 'ZGS': 1}
          Classifications: {'undetermined': 17}
          Link IDs: {None: 16}
          Unresolved non-hydrogen bonds: 97
          Unresolved non-hydrogen angles: 146
          Unresolved non-hydrogen dihedrals: 210
          Unresolved non-hydrogen chiralities: 41
          bond proxies already assigned to first conformer: 417
    Chain: "B"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 35
          Unusual residues: {'LMT': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Residues with excluded nonbonded symmetry interactions: 5
    residue:
      pdb=" N  AGLN A 345 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NE2BGLN A 345 " occ=0.50
    residue:
      pdb=" N  ATRP A 400 " occ=0.50
      ... (26 atoms not shown)
      pdb=" CH2BTRP A 400 " occ=0.50
    residue:
      pdb=" N  APHE A 449 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE A 449 " occ=0.50
    residue:
      pdb=" C1 ALMT A 602 " occ=0.50
      ... (46 atoms not shown)
      pdb=" O6'BLMT A 602 " occ=0.50
    residue:
      pdb=" C1 ALMT A 608 " occ=0.50
      ... (68 atoms not shown)
      pdb=" O6BBLMT A 608 " occ=0.50
  Time building chain proxies: 7.23, per 1000 atoms: 1.05
  Number of scatterers: 6862
  At special positions: 0
  Unit cell: (69.208, 74.272, 142.636, 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      38     16.00
     P       1     15.00
     Na      1     11.00
     O    1295      8.00
     N    1023      7.00
     C    4504      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: 2.01
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 10 sheets defined
      45.3% alpha, 18.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.84
  Creating SS restraints...
    Processing helix  chain 'A' and resid 36 through 46
    Processing helix  chain 'A' and resid 47 through 68
      removed outlier: 3.835A  pdb=" N   GLN A  51 " --> pdb=" O   GLY A  47 " (cutoff:3.500A)
      removed outlier: 6.093A  pdb=" N   GLN A  62 " --> pdb=" O   GLY A  58 " (cutoff:3.500A)
      removed outlier: 5.307A  pdb=" N   ILE A  63 " --> pdb=" O   PHE A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 100
      removed outlier: 3.958A  pdb=" N   ARG A  84 " --> pdb=" O   LEU A  80 " (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: 3.630A  pdb=" N   LEU A 122 " --> pdb=" O   PRO A 118 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   TRP A 128 " --> pdb=" O   TYR A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 162
      removed outlier: 3.645A  pdb=" N   TRP A 140 " --> pdb=" O   GLY A 136 " (cutoff:3.500A)
      Proline residue:  A 158  - end of helix
    Processing helix  chain 'A' and resid 162 through 167
      removed outlier: 4.511A  pdb=" N   SER A 167 " --> pdb=" O   THR A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 200
      removed outlier: 3.810A  pdb=" N   THR A 192 " --> pdb=" O   THR A 188 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   GLN A 195 " --> pdb=" O   GLY A 191 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLY A 196 " --> pdb=" O   THR A 192 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   GLN A 197 " --> pdb=" O   ALA A 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 262
      removed outlier: 3.502A  pdb=" N   VAL A 262 " --> pdb=" O   LEU A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 288
      removed outlier: 3.510A  pdb=" N   HIS A 288 " --> pdb=" O   MET A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 319
      removed outlier: 4.862A  pdb=" N   ALA A 313 " --> pdb=" O   GLU A 309 " (cutoff:3.500A)
      removed outlier: 5.335A  pdb=" N   LEU A 314 " --> pdb=" O   GLY A 310 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   PHE A 315 " --> pdb=" O   ASN A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 340
      removed outlier: 3.657A  pdb=" N   VAL A 329 " --> pdb=" O   ASP A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 351
      removed outlier: 3.862A  pdb=" N   THR A 349 " --> pdb=" O  AGLN A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 353 through 361
      removed outlier: 3.974A  pdb=" N   THR A 361 " --> pdb=" O   VAL A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 373
      removed outlier: 4.520A  pdb=" N   PHE A 367 " --> pdb=" O   SER A 363 " (cutoff:3.500A)
      removed outlier: 3.922A  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: 3.851A  pdb=" N   SER A 436 " --> pdb=" O   THR A 432 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 473
    Processing helix  chain 'A' and resid 473 through 488
      removed outlier: 3.503A  pdb=" N   SER A 488 " --> pdb=" O   LEU A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 493 through 507
      removed outlier: 3.636A  pdb=" N   GLN A 497 " --> pdb=" O   GLU A 493 " (cutoff:3.500A)
      removed outlier: 5.067A  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 11 through 12
      removed outlier: 6.023A  pdb=" N   LYS B  11 " --> pdb=" O   ASN B 102 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   VAL B  32 " --> pdb=" O   TYR B  48 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   TYR B  48 " --> pdb=" O   VAL B  32 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   TRP B  34 " --> pdb=" O   LEU B  46 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 18 through 22
    Processing sheet with id=AA3, first strand: chain 'B' and resid 112 through 114
      removed outlier: 3.889A  pdb=" N   ASN B 134 " --> pdb=" O   TYR B 166 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   TYR B 166 " --> pdb=" O   ASN B 134 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 148 through 149
      removed outlier: 4.861A  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 33 through 39
      removed outlier: 6.644A  pdb=" N   VAL C  34 " --> pdb=" O   ALA C  49 " (cutoff:3.500A)
      removed outlier: 4.875A  pdb=" N   ALA C  49 " --> pdb=" O   VAL C  34 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   TRP C  36 " --> pdb=" O   PRO C  47 " (cutoff:3.500A)
    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: 5.997A  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: 5.997A  pdb=" N   TRP C 170 " --> pdb=" O   GLY C 143 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   LEU C 169 " --> pdb=" O   ASN C 166 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 149 through 151
      removed outlier: 4.779A  pdb=" N   ALA C 184 " --> pdb=" O   VAL C 200 " (cutoff:3.500A)

    388 hydrogen bonds defined for protein.
    1100 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: 2.14

  Time building geometry restraints manager: 2.31 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 996
        1.30 -     1.43: 1851
        1.43 -     1.56: 4027
        1.56 -     1.68: 111
        1.68 -     1.81: 55
  Bond restraints: 7040
  Sorted by residual:
  bond pdb=" C1B LMT A 612 "
       pdb=" O5B LMT A 612 "
    ideal  model  delta    sigma   weight residual
    1.393  1.521 -0.128 2.00e-02 2.50e+03 4.12e+01
  bond pdb=" C1BALMT A 608 "
       pdb=" O5BALMT A 608 "
    ideal  model  delta    sigma   weight residual
    1.393  1.517 -0.124 2.00e-02 2.50e+03 3.83e+01
  bond pdb=" C1BBLMT A 608 "
       pdb=" O5BBLMT A 608 "
    ideal  model  delta    sigma   weight residual
    1.393  1.515 -0.122 2.00e-02 2.50e+03 3.74e+01
  bond pdb=" C1B LMT A 611 "
       pdb=" O5B LMT A 611 "
    ideal  model  delta    sigma   weight residual
    1.393  1.514 -0.121 2.00e-02 2.50e+03 3.69e+01
  bond pdb=" C1B LMT A 616 "
       pdb=" O5B LMT A 616 "
    ideal  model  delta    sigma   weight residual
    1.393  1.514 -0.121 2.00e-02 2.50e+03 3.68e+01
  ... (remaining 7035 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.86: 9423
        5.86 -    11.72: 140
       11.72 -    17.58: 5
       17.58 -    23.44: 1
       23.44 -    29.30: 2
  Bond angle restraints: 9571
  Sorted by residual:
  angle pdb=" C09 ZGS A 601 "
        pdb=" C10 ZGS A 601 "
        pdb=" C11 ZGS A 601 "
      ideal   model   delta    sigma   weight residual
     127.16  156.46  -29.30 3.00e+00 1.11e-01 9.54e+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  151.01  -23.49 3.00e+00 1.11e-01 6.13e+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  132.09  -21.39 3.00e+00 1.11e-01 5.08e+01
  angle pdb=" C03 ZGS A 601 "
        pdb=" C04 ZGS A 601 "
        pdb=" C05 ZGS A 601 "
      ideal   model   delta    sigma   weight residual
     127.34  142.92  -15.58 3.00e+00 1.11e-01 2.70e+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  112.16   15.51 3.00e+00 1.11e-01 2.67e+01
  ... (remaining 9566 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.52: 4087
       23.52 -    47.03: 262
       47.03 -    70.55: 99
       70.55 -    94.07: 56
       94.07 -   117.58: 96
  Dihedral angle restraints: 4600
    sinusoidal: 2136
      harmonic: 2464
  Sorted by residual:
  dihedral pdb=" CA  LEU B 132 "
           pdb=" C   LEU B 132 "
           pdb=" N   PRO B 133 "
           pdb=" CA  PRO B 133 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.19  -19.81     0      5.00e+00 4.00e-02 1.57e+01
  dihedral pdb=" C5B LMT A 604 "
           pdb=" C1B LMT A 604 "
           pdb=" O5B LMT A 604 "
           pdb=" O1B LMT A 604 "
      ideal   model   delta sinusoidal    sigma   weight residual
     295.61  178.03  117.58     1      3.00e+01 1.11e-03 1.56e+01
  dihedral pdb=" C2B LMT A 604 "
           pdb=" C1B LMT A 604 "
           pdb=" O5B LMT A 604 "
           pdb=" C5B LMT A 604 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -57.12   59.92 -117.04     1      3.00e+01 1.11e-03 1.55e+01
  ... (remaining 4597 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 898
       0.060 -    0.120: 195
       0.120 -    0.180: 42
       0.180 -    0.240: 3
       0.240 -    0.300: 2
  Chirality restraints: 1140
  Sorted by residual:
  chirality pdb=" C1B LMT B 301 "
            pdb=" C2B LMT B 301 "
            pdb=" O1B LMT B 301 "
            pdb=" O5B LMT B 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.20   -2.50    0.30 2.00e-01 2.50e+01 2.25e+00
  chirality pdb=" C4' LMT B 301 "
            pdb=" C3' LMT B 301 "
            pdb=" C5' LMT B 301 "
            pdb=" O1B LMT B 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.55   -2.26   -0.29 2.00e-01 2.50e+01 2.13e+00
  chirality pdb=" C1B LMT A 605 "
            pdb=" C2B LMT A 605 "
            pdb=" O1B LMT A 605 "
            pdb=" O5B LMT A 605 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.20   -2.42    0.22 2.00e-01 2.50e+01 1.25e+00
  ... (remaining 1137 not shown)

  Planarity restraints: 1132
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 398 "   -0.045 5.00e-02 4.00e+02   6.65e-02 7.09e+00
        pdb=" N   PRO A 399 "    0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO A 399 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 399 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP C  46 "   -0.042 5.00e-02 4.00e+02   6.40e-02 6.56e+00
        pdb=" N   PRO C  47 "    0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO C  47 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO C  47 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 374 "   -0.038 5.00e-02 4.00e+02   5.81e-02 5.40e+00
        pdb=" N   PRO A 375 "    0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO A 375 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 375 "   -0.032 5.00e-02 4.00e+02
  ... (remaining 1129 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.85: 2310
        2.85 -     3.37: 6004
        3.37 -     3.88: 11522
        3.88 -     4.39: 12717
        4.39 -     4.90: 22541
  Nonbonded interactions: 55094
  Sorted by model distance:
  nonbonded pdb=" O   TYR A  43 "
            pdb=" OH  TYR A 159 "
     model   vdw
     2.344 3.040
  nonbonded pdb=" O   THR A 381 "
            pdb=" OG  SER A 385 "
     model   vdw
     2.347 3.040
  nonbonded pdb=" O   SER A 439 "
            pdb=" OG  SER A 443 "
     model   vdw
     2.354 3.040
  nonbonded pdb=" O   SER A 132 "
            pdb=" O2B LMT A 607 "
     model   vdw
     2.362 3.040
  nonbonded pdb=" OH  TYR A  43 "
            pdb=" OG1 THR A 163 "
     model   vdw
     2.372 3.040
  ... (remaining 55089 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.440
  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:             0.000
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     23.980
  Find NCS groups from input model:        0.090
  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:             0.010
  Load rotamer database and sin/cos tables:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
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   0.128   7044  Z= 0.615
  Angle     :  1.445  29.303   9579  Z= 0.602
  Chirality :  0.054   0.300   1140
  Planarity :  0.007   0.067   1132
  Dihedral  : 27.080 117.582   3018
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.54 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  :  7.06 %
    Favored  : 91.95 %
  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: -2.64 (0.24), residues: 865
  helix: -1.03 (0.22), residues: 367
  sheet: -1.07 (0.38), residues: 170
  loop : -2.88 (0.28), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 140 
 HIS   0.003   0.001   HIS A 156 
 PHE   0.031   0.002   PHE C  38 
 TYR   0.017   0.002   TYR A  50 
 ARG   0.001   0.000   ARG C  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12769 (  375)
  hydrogen bonds       : angle       7.06443 ( 1100)
  SS BOND              : bond        0.00322 (    4)
  SS BOND              : angle       0.94582 (    8)
  covalent geometry    : bond        0.01227 ( 7040)
  covalent geometry    : angle       1.44504 ( 9571)

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

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 142
  time to evaluate  : 0.687 
Fit side-chains
REVERT: A  276 MET cc_start: 0.6336 (mmm) cc_final: 0.5739 (mmm)
REVERT: A  339 LEU cc_start: 0.7642 (mt) cc_final: 0.7297 (mt)
REVERT: B   61 SER cc_start: 0.8006 (m) cc_final: 0.7796 (p)
REVERT: B   91 LYS cc_start: 0.8375 (mttt) cc_final: 0.8109 (mtpt)
REVERT: C   13 ARG cc_start: 0.7831 (ttm-80) cc_final: 0.7594 (mmt-90)
REVERT: C   23 LYS cc_start: 0.7936 (tttm) cc_final: 0.7612 (mtpt)
  outliers start: 6
  outliers final: 1
  residues processed: 147
  average time/residue: 0.1956
  time to fit residues: 37.9157
Evaluate side-chains
  104 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 103
  time to evaluate  : 0.644 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 VAL
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:    0.0470
   chunk 36 optimal weight:    5.9990
   chunk 22 optimal weight:   10.0000
   chunk 43 optimal weight:    1.9990
   chunk 34 optimal weight:    0.5980
   chunk 67 optimal weight:    0.0870
   chunk 26 optimal weight:    0.5980
   chunk 40 optimal weight:    1.9990
   chunk 50 optimal weight:    0.1980
   chunk 78 optimal weight:    0.9980
   overall best weight:    0.3056

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

Flipped N/Q/H residues before XYZ refinement:
A 149 GLN
** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  36 ASN
B 102 ASN
B 110 GLN
C  50 ASN
C  57 GLN
C  74 GLN
C  99 ASN
C 166 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.179247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.142610 restraints weight = 19901.808|
|-----------------------------------------------------------------------------|
r_work (start): 0.3641 rms_B_bonded: 4.50
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3638
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3638 r_free = 0.3638    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 = 0.3637 r_free = 0.3637    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3637
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.1877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   7044  Z= 0.149
  Angle     :  0.806   9.522   9579  Z= 0.351
  Chirality :  0.048   0.264   1140
  Planarity :  0.006   0.058   1132
  Dihedral  : 18.893  78.201   1806
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 13.79 %
    Favored  : 84.73 %
  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: -1.15 (0.27), residues: 865
  helix:  0.65 (0.25), residues: 386
  sheet: -1.17 (0.35), residues: 198
  loop : -2.39 (0.33), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 103 
 HIS   0.002   0.001   HIS A 420 
 PHE   0.017   0.002   PHE A 427 
 TYR   0.009   0.001   TYR A 251 
 ARG   0.005   0.001   ARG A 108 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03526 (  375)
  hydrogen bonds       : angle       4.70462 ( 1100)
  SS BOND              : bond        0.00158 (    4)
  SS BOND              : angle       0.36500 (    8)
  covalent geometry    : bond        0.00319 ( 7040)
  covalent geometry    : angle       0.80634 ( 9571)

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

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 109
  time to evaluate  : 0.667 
Fit side-chains
REVERT: A  103 TRP cc_start: 0.8343 (t-100) cc_final: 0.8052 (t60)
REVERT: A  108 ARG cc_start: 0.7586 (mtp180) cc_final: 0.7314 (mtp180)
REVERT: A  276 MET cc_start: 0.6415 (mmm) cc_final: 0.6025 (mmt)
REVERT: A  411 LYS cc_start: 0.8207 (tmmt) cc_final: 0.7900 (tmtt)
REVERT: B   91 LYS cc_start: 0.8284 (mttt) cc_final: 0.8080 (mtpt)
REVERT: C   81 ILE cc_start: 0.8418 (mm) cc_final: 0.8109 (mm)
REVERT: C   95 TRP cc_start: 0.7451 (p-90) cc_final: 0.7197 (p-90)
  outliers start: 9
  outliers final: 3
  residues processed: 113
  average time/residue: 0.2920
  time to fit residues: 43.0189
Evaluate side-chains
  102 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 99
  time to evaluate  : 1.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain C residue  169 LEU
Chi-restraints excluded: chain C residue  196 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 54 optimal weight:    0.0870
   chunk 73 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 49 optimal weight:    0.0670
   chunk 21 optimal weight:    0.9990
   chunk 68 optimal weight:    0.8980
   overall best weight:    0.5296

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

Flipped N/Q/H residues before XYZ refinement:
A 152 GLN
** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 153 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 = 0.175014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.138766 restraints weight = 23165.865|
|-----------------------------------------------------------------------------|
r_work (start): 0.3592 rms_B_bonded: 4.87
r_work (final): 0.3592
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3592
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3592 r_free = 0.3592    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3592 r_free = 0.3592    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3592
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.2266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   7044  Z= 0.154
  Angle     :  0.675   8.413   9579  Z= 0.314
  Chirality :  0.043   0.236   1140
  Planarity :  0.005   0.061   1132
  Dihedral  : 12.803  59.547   1805
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 14.45 %
    Favored  : 83.58 %
  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: -0.73 (0.28), residues: 865
  helix:  1.28 (0.26), residues: 383
  sheet: -1.15 (0.37), residues: 176
  loop : -2.39 (0.32), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 140 
 HIS   0.003   0.001   HIS A 156 
 PHE   0.018   0.002   PHE B  89 
 TYR   0.013   0.001   TYR A 251 
 ARG   0.002   0.000   ARG A 108 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03533 (  375)
  hydrogen bonds       : angle       4.49705 ( 1100)
  SS BOND              : bond        0.00212 (    4)
  SS BOND              : angle       0.31193 (    8)
  covalent geometry    : bond        0.00363 ( 7040)
  covalent geometry    : angle       0.67477 ( 9571)

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

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 0.684 
Fit side-chains
REVERT: A  276 MET cc_start: 0.6520 (mmm) cc_final: 0.6028 (mmt)
REVERT: A  411 LYS cc_start: 0.8256 (tmmt) cc_final: 0.7961 (tmtt)
REVERT: B   91 LYS cc_start: 0.8353 (mttt) cc_final: 0.8074 (mtpt)
REVERT: B  105 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6306 (tm-30)
REVERT: C   81 ILE cc_start: 0.8469 (mm) cc_final: 0.8138 (mm)
REVERT: C   95 TRP cc_start: 0.7716 (p-90) cc_final: 0.7340 (p-90)
  outliers start: 12
  outliers final: 9
  residues processed: 113
  average time/residue: 0.2061
  time to fit residues: 30.6278
Evaluate side-chains
  118 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 108
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 ASP
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain B residue    4 ILE
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain C residue  163 SER
Chi-restraints excluded: chain C residue  166 ASN
Chi-restraints excluded: chain C residue  169 LEU
Chi-restraints excluded: chain C residue  196 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 53 optimal weight:    0.3980
   chunk 70 optimal weight:    0.2980
   chunk 2 optimal weight:    0.8980
   chunk 81 optimal weight:    0.0170
   chunk 20 optimal weight:    0.5980
   chunk 27 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 28 optimal weight:    0.6980
   chunk 47 optimal weight:    0.2980
   chunk 35 optimal weight:    0.7980
   overall best weight:    0.3218

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

Flipped N/Q/H residues before XYZ refinement:
** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 153 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.176378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.151528 restraints weight = 27777.628|
|-----------------------------------------------------------------------------|
r_work (start): 0.3733 rms_B_bonded: 3.35
r_work: 0.3225 rms_B_bonded: 4.87 restraints_weight: 0.5000
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3233
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3233 r_free = 0.3233    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3232 r_free = 0.3232    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3232
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.2535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7044  Z= 0.118
  Angle     :  0.599   6.403   9579  Z= 0.284
  Chirality :  0.041   0.270   1140
  Planarity :  0.005   0.061   1132
  Dihedral  : 11.469  59.462   1805
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 14.78 %
    Favored  : 82.92 %
  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: -0.42 (0.29), residues: 865
  helix:  1.54 (0.26), residues: 389
  sheet: -1.11 (0.36), residues: 199
  loop : -2.28 (0.34), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 103 
 HIS   0.001   0.001   HIS A 156 
 PHE   0.017   0.001   PHE A 298 
 TYR   0.010   0.001   TYR A 251 
 ARG   0.001   0.000   ARG A 108 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03171 (  375)
  hydrogen bonds       : angle       4.21978 ( 1100)
  SS BOND              : bond        0.00242 (    4)
  SS BOND              : angle       0.29351 (    8)
  covalent geometry    : bond        0.00269 ( 7040)
  covalent geometry    : angle       0.59881 ( 9571)

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

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 107
  time to evaluate  : 0.889 
Fit side-chains
REVERT: A  103 TRP cc_start: 0.7889 (t-100) cc_final: 0.7572 (t60)
REVERT: A  170 GLN cc_start: 0.8246 (tp40) cc_final: 0.7840 (tp-100)
REVERT: A  263 LYS cc_start: 0.8337 (mmtt) cc_final: 0.7739 (mmpt)
REVERT: A  276 MET cc_start: 0.6227 (mmm) cc_final: 0.5669 (mmt)
REVERT: A  303 LEU cc_start: 0.8835 (mt) cc_final: 0.8576 (mp)
REVERT: A  347 PHE cc_start: 0.8566 (t80) cc_final: 0.8235 (t80)
REVERT: A  411 LYS cc_start: 0.8755 (tmmt) cc_final: 0.8422 (tmtt)
REVERT: B   91 LYS cc_start: 0.8740 (mttt) cc_final: 0.8351 (mtpt)
REVERT: B  105 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.6139 (tm-30)
REVERT: B  200 LEU cc_start: 0.6966 (OUTLIER) cc_final: 0.6688 (pt)
REVERT: C   81 ILE cc_start: 0.8497 (mm) cc_final: 0.8209 (mm)
REVERT: C   95 TRP cc_start: 0.8332 (p-90) cc_final: 0.7775 (p-90)
  outliers start: 14
  outliers final: 9
  residues processed: 115
  average time/residue: 0.2172
  time to fit residues: 33.5880
Evaluate side-chains
  113 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 102
  time to evaluate  : 0.681 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  333 ILE
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain B residue    4 ILE
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain C residue   17 SER
Chi-restraints excluded: chain C residue   20 ILE
Chi-restraints excluded: chain C residue   90 THR
Chi-restraints excluded: chain C residue  169 LEU
Chi-restraints excluded: chain C residue  196 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 78 optimal weight:    0.0970
   chunk 70 optimal weight:    0.8980
   chunk 37 optimal weight:    0.8980
   chunk 4 optimal weight:    0.0980
   chunk 82 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 57 optimal weight:    1.9990
   chunk 74 optimal weight:    4.9990
   chunk 2 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 153 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.173608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.142294 restraints weight = 16502.640|
|-----------------------------------------------------------------------------|
r_work (start): 0.3596 rms_B_bonded: 2.92
r_work: 0.3220 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3258
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3258 r_free = 0.3258    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3258 r_free = 0.3258    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3258
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.2674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   7044  Z= 0.147
  Angle     :  0.608   6.765   9579  Z= 0.292
  Chirality :  0.041   0.202   1140
  Planarity :  0.005   0.063   1132
  Dihedral  : 10.927  59.869   1805
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 14.12 %
    Favored  : 82.43 %
  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: -0.35 (0.29), residues: 865
  helix:  1.65 (0.26), residues: 385
  sheet: -0.98 (0.37), residues: 197
  loop : -2.34 (0.34), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 140 
 HIS   0.002   0.001   HIS A 156 
 PHE   0.019   0.001   PHE B  89 
 TYR   0.012   0.001   TYR A 251 
 ARG   0.002   0.000   ARG A 455 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03375 (  375)
  hydrogen bonds       : angle       4.30208 ( 1100)
  SS BOND              : bond        0.00219 (    4)
  SS BOND              : angle       0.35746 (    8)
  covalent geometry    : bond        0.00346 ( 7040)
  covalent geometry    : angle       0.60859 ( 9571)

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

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 109
  time to evaluate  : 0.769 
Fit side-chains
REVERT: A  103 TRP cc_start: 0.7870 (t-100) cc_final: 0.7553 (t60)
REVERT: A  170 GLN cc_start: 0.8310 (tp40) cc_final: 0.7870 (tp-100)
REVERT: A  263 LYS cc_start: 0.8312 (mmtt) cc_final: 0.7775 (mmpt)
REVERT: A  276 MET cc_start: 0.6214 (mmm) cc_final: 0.5624 (mmt)
REVERT: A  303 LEU cc_start: 0.8807 (mt) cc_final: 0.8546 (mp)
REVERT: A  411 LYS cc_start: 0.8827 (tmmt) cc_final: 0.8614 (tmtt)
REVERT: B   91 LYS cc_start: 0.8757 (mttt) cc_final: 0.8356 (mtpt)
REVERT: B  105 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.5904 (tm-30)
REVERT: B  200 LEU cc_start: 0.6889 (OUTLIER) cc_final: 0.6590 (pt)
REVERT: C   23 LYS cc_start: 0.8198 (tttm) cc_final: 0.7942 (mtpt)
REVERT: C   81 ILE cc_start: 0.8429 (mm) cc_final: 0.8119 (mm)
REVERT: C   95 TRP cc_start: 0.8291 (p-90) cc_final: 0.7771 (p-90)
  outliers start: 21
  outliers final: 14
  residues processed: 121
  average time/residue: 0.2228
  time to fit residues: 35.1801
Evaluate side-chains
  123 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 0.706 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 ASP
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  333 ILE
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain B residue    4 ILE
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain C residue   17 SER
Chi-restraints excluded: chain C residue   20 ILE
Chi-restraints excluded: chain C residue   90 THR
Chi-restraints excluded: chain C residue  163 SER
Chi-restraints excluded: chain C residue  166 ASN
Chi-restraints excluded: chain C residue  169 LEU
Chi-restraints excluded: chain C residue  196 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 11 optimal weight:    0.9980
   chunk 36 optimal weight:    0.7980
   chunk 17 optimal weight:    0.8980
   chunk 64 optimal weight:   20.0000
   chunk 79 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 12 optimal weight:    0.5980
   chunk 77 optimal weight:    0.2980
   chunk 3 optimal weight:    0.8980
   chunk 45 optimal weight:   10.0000
   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 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 153 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.171936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.144233 restraints weight = 26517.602|
|-----------------------------------------------------------------------------|
r_work (start): 0.3652 rms_B_bonded: 3.63
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3609
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3609 r_free = 0.3609    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3609 r_free = 0.3609    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3609
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.2872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   7044  Z= 0.175
  Angle     :  0.630   7.893   9579  Z= 0.306
  Chirality :  0.042   0.202   1140
  Planarity :  0.005   0.066   1132
  Dihedral  : 10.794  59.060   1805
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.96 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 14.45 %
    Favored  : 82.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.29), residues: 865
  helix:  1.63 (0.26), residues: 385
  sheet: -0.95 (0.37), residues: 197
  loop : -2.31 (0.34), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP C  36 
 HIS   0.003   0.001   HIS A 156 
 PHE   0.020   0.002   PHE B  89 
 TYR   0.012   0.001   TYR A 251 
 ARG   0.001   0.000   ARG A 455 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03484 (  375)
  hydrogen bonds       : angle       4.36654 ( 1100)
  SS BOND              : bond        0.00211 (    4)
  SS BOND              : angle       0.91592 (    8)
  covalent geometry    : bond        0.00419 ( 7040)
  covalent geometry    : angle       0.62959 ( 9571)

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

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 0.689 
Fit side-chains
REVERT: A  263 LYS cc_start: 0.8250 (mmtt) cc_final: 0.7802 (mmpt)
REVERT: A  276 MET cc_start: 0.6371 (mmm) cc_final: 0.5864 (mmt)
REVERT: A  303 LEU cc_start: 0.8930 (mt) cc_final: 0.8671 (mp)
REVERT: B   91 LYS cc_start: 0.8422 (mttt) cc_final: 0.8048 (mtpt)
REVERT: B  105 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.6045 (tm-30)
REVERT: B  200 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.7072 (pt)
REVERT: C   81 ILE cc_start: 0.8453 (mm) cc_final: 0.8101 (mm)
REVERT: C   95 TRP cc_start: 0.7940 (p-90) cc_final: 0.7508 (p-90)
  outliers start: 20
  outliers final: 15
  residues processed: 115
  average time/residue: 0.2175
  time to fit residues: 32.7944
Evaluate side-chains
  120 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 ASP
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  333 ILE
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain B residue    4 ILE
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain C residue   13 ARG
Chi-restraints excluded: chain C residue   17 SER
Chi-restraints excluded: chain C residue   20 ILE
Chi-restraints excluded: chain C residue   90 THR
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  163 SER
Chi-restraints excluded: chain C residue  169 LEU
Chi-restraints excluded: chain C residue  196 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 44 optimal weight:    0.4980
   chunk 59 optimal weight:    0.6980
   chunk 28 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9980
   chunk 2 optimal weight:    0.6980
   chunk 60 optimal weight:    2.9990
   chunk 26 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0030
   chunk 63 optimal weight:    2.9990
   overall best weight:    0.4990

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

Flipped N/Q/H residues before XYZ refinement:
** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 153 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 = 0.172940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.141078 restraints weight = 20301.597|
|-----------------------------------------------------------------------------|
r_work (start): 0.3579 rms_B_bonded: 3.64
r_work: 0.3154 rms_B_bonded: 4.70 restraints_weight: 0.5000
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3171
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3171 r_free = 0.3171    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3171 r_free = 0.3171    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3171
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.2925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   7044  Z= 0.143
  Angle     :  0.601   7.378   9579  Z= 0.291
  Chirality :  0.040   0.188   1140
  Planarity :  0.005   0.066   1132
  Dihedral  : 10.526  58.112   1805
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 15.27 %
    Favored  : 81.61 %
  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: -0.25 (0.29), residues: 865
  helix:  1.77 (0.26), residues: 382
  sheet: -0.90 (0.37), residues: 202
  loop : -2.36 (0.34), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 344 
 HIS   0.002   0.001   HIS A 156 
 PHE   0.017   0.001   PHE A 298 
 TYR   0.011   0.001   TYR A 251 
 ARG   0.002   0.000   ARG A 455 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03332 (  375)
  hydrogen bonds       : angle       4.32265 ( 1100)
  SS BOND              : bond        0.00275 (    4)
  SS BOND              : angle       0.87053 (    8)
  covalent geometry    : bond        0.00338 ( 7040)
  covalent geometry    : angle       0.60121 ( 9571)

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

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 100
  time to evaluate  : 0.639 
Fit side-chains
REVERT: A  170 GLN cc_start: 0.8134 (tp40) cc_final: 0.7781 (tp-100)
REVERT: A  263 LYS cc_start: 0.8320 (mmtt) cc_final: 0.7860 (mmpt)
REVERT: A  276 MET cc_start: 0.6235 (mmm) cc_final: 0.5639 (mmt)
REVERT: A  303 LEU cc_start: 0.8869 (mt) cc_final: 0.8609 (mp)
REVERT: B   91 LYS cc_start: 0.8758 (mttt) cc_final: 0.8370 (mtpt)
REVERT: B  105 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.6746 (tt0)
REVERT: B  200 LEU cc_start: 0.7104 (OUTLIER) cc_final: 0.6752 (pt)
REVERT: C   81 ILE cc_start: 0.8444 (mm) cc_final: 0.8114 (mm)
REVERT: C   95 TRP cc_start: 0.8366 (p-90) cc_final: 0.7870 (p-90)
  outliers start: 19
  outliers final: 15
  residues processed: 111
  average time/residue: 0.2007
  time to fit residues: 29.3966
Evaluate side-chains
  116 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 99
  time to evaluate  : 0.636 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 ASP
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  333 ILE
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain B residue    4 ILE
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain C residue   13 ARG
Chi-restraints excluded: chain C residue   17 SER
Chi-restraints excluded: chain C residue   90 THR
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  163 SER
Chi-restraints excluded: chain C residue  169 LEU
Chi-restraints excluded: chain C residue  196 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 41 optimal weight:    0.1980
   chunk 51 optimal weight:    0.5980
   chunk 58 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 45 optimal weight:    5.9990
   chunk 64 optimal weight:   10.0000
   chunk 23 optimal weight:    7.9990
   chunk 81 optimal weight:    0.3980
   chunk 71 optimal weight:    0.2980
   chunk 83 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   overall best weight:    0.4982

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

Flipped N/Q/H residues before XYZ refinement:
** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.173209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.135331 restraints weight = 24956.403|
|-----------------------------------------------------------------------------|
r_work (start): 0.3542 rms_B_bonded: 5.64
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3545
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3545 r_free = 0.3545    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3546 r_free = 0.3546    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3546
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.3016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   7044  Z= 0.144
  Angle     :  0.603   7.953   9579  Z= 0.294
  Chirality :  0.040   0.180   1140
  Planarity :  0.005   0.066   1132
  Dihedral  : 10.335  59.683   1805
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.96 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 14.94 %
    Favored  : 81.94 %
  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: -0.21 (0.29), residues: 865
  helix:  1.82 (0.26), residues: 383
  sheet: -0.89 (0.37), residues: 202
  loop : -2.39 (0.34), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 344 
 HIS   0.002   0.001   HIS A 156 
 PHE   0.017   0.001   PHE C  38 
 TYR   0.011   0.001   TYR A 251 
 ARG   0.001   0.000   ARG A 455 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03331 (  375)
  hydrogen bonds       : angle       4.30308 ( 1100)
  SS BOND              : bond        0.00237 (    4)
  SS BOND              : angle       0.77809 (    8)
  covalent geometry    : bond        0.00339 ( 7040)
  covalent geometry    : angle       0.60263 ( 9571)

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

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 101
  time to evaluate  : 0.642 
Fit side-chains
REVERT: A  170 GLN cc_start: 0.8226 (tp40) cc_final: 0.7838 (tp-100)
REVERT: A  263 LYS cc_start: 0.8328 (mmtt) cc_final: 0.7916 (mmpt)
REVERT: A  276 MET cc_start: 0.6581 (mmm) cc_final: 0.6007 (mmt)
REVERT: A  303 LEU cc_start: 0.8936 (mt) cc_final: 0.8679 (mp)
REVERT: B   91 LYS cc_start: 0.8334 (mttt) cc_final: 0.8066 (mtpt)
REVERT: B  105 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.6508 (tt0)
REVERT: B  200 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.7026 (pt)
REVERT: C   81 ILE cc_start: 0.8449 (mm) cc_final: 0.8102 (mm)
REVERT: C   95 TRP cc_start: 0.7742 (p-90) cc_final: 0.7409 (p-90)
  outliers start: 19
  outliers final: 15
  residues processed: 111
  average time/residue: 0.2132
  time to fit residues: 30.7246
Evaluate side-chains
  118 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 101
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 ASP
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  333 ILE
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain B residue    4 ILE
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain C residue   13 ARG
Chi-restraints excluded: chain C residue   17 SER
Chi-restraints excluded: chain C residue   90 THR
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  163 SER
Chi-restraints excluded: chain C residue  169 LEU
Chi-restraints excluded: chain C residue  196 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 18 optimal weight:    0.4980
   chunk 38 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9980
   chunk 27 optimal weight:    0.5980
   chunk 47 optimal weight:    2.9990
   chunk 76 optimal weight:    0.3980
   chunk 40 optimal weight:    0.0980
   chunk 66 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.173646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.134963 restraints weight = 28938.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.3540 rms_B_bonded: 6.31
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3539
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3539 r_free = 0.3539    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3539 r_free = 0.3539    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3539
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.3056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   7044  Z= 0.136
  Angle     :  0.591   8.098   9579  Z= 0.288
  Chirality :  0.040   0.171   1140
  Planarity :  0.005   0.066   1132
  Dihedral  : 10.083  59.416   1805
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 15.11 %
    Favored  : 81.94 %
  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: -0.16 (0.29), residues: 865
  helix:  1.89 (0.26), residues: 382
  sheet: -0.88 (0.37), residues: 202
  loop : -2.37 (0.34), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 344 
 HIS   0.002   0.001   HIS A 156 
 PHE   0.016   0.001   PHE C  38 
 TYR   0.011   0.001   TYR A 251 
 ARG   0.001   0.000   ARG A 455 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03265 (  375)
  hydrogen bonds       : angle       4.25799 ( 1100)
  SS BOND              : bond        0.00230 (    4)
  SS BOND              : angle       0.71669 (    8)
  covalent geometry    : bond        0.00320 ( 7040)
  covalent geometry    : angle       0.59086 ( 9571)

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

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 99
  time to evaluate  : 0.616 
Fit side-chains
REVERT: A  170 GLN cc_start: 0.8223 (tp40) cc_final: 0.7818 (tp-100)
REVERT: A  263 LYS cc_start: 0.8345 (mmtt) cc_final: 0.8002 (mmpt)
REVERT: A  276 MET cc_start: 0.6626 (mmm) cc_final: 0.6038 (mmt)
REVERT: A  303 LEU cc_start: 0.8949 (mt) cc_final: 0.8702 (mp)
REVERT: B   91 LYS cc_start: 0.8316 (mttt) cc_final: 0.8049 (mtpt)
REVERT: B  105 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.6345 (tt0)
REVERT: B  155 SER cc_start: 0.8751 (p) cc_final: 0.8252 (t)
REVERT: B  200 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.6988 (pt)
REVERT: C   81 ILE cc_start: 0.8457 (mm) cc_final: 0.8119 (mm)
REVERT: C   95 TRP cc_start: 0.7826 (p-90) cc_final: 0.7533 (p-90)
  outliers start: 18
  outliers final: 13
  residues processed: 108
  average time/residue: 0.2203
  time to fit residues: 31.2984
Evaluate side-chains
  118 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 0.760 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  333 ILE
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain B residue    4 ILE
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain C residue   13 ARG
Chi-restraints excluded: chain C residue   17 SER
Chi-restraints excluded: chain C residue   90 THR
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  163 SER
Chi-restraints excluded: chain C residue  196 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 68 optimal weight:    0.6980
   chunk 50 optimal weight:    0.0980
   chunk 75 optimal weight:    0.5980
   chunk 70 optimal weight:    0.6980
   chunk 41 optimal weight:    0.0470
   chunk 21 optimal weight:    0.9980
   chunk 19 optimal weight:    0.7980
   chunk 8 optimal weight:    0.0770
   chunk 57 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 60 optimal weight:    0.6980
   overall best weight:    0.3036

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

Flipped N/Q/H residues before XYZ refinement:
** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  26 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.175407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.136469 restraints weight = 22239.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.3561 rms_B_bonded: 5.47
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3551
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3551 r_free = 0.3551    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3551 r_free = 0.3551    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3551
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.3123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7044  Z= 0.117
  Angle     :  0.575   7.758   9579  Z= 0.280
  Chirality :  0.039   0.158   1140
  Planarity :  0.005   0.066   1132
  Dihedral  :  9.783  59.948   1805
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 16.09 %
    Favored  : 81.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.29), residues: 865
  helix:  1.96 (0.26), residues: 385
  sheet: -0.92 (0.36), residues: 205
  loop : -2.34 (0.35), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 344 
 HIS   0.002   0.001   HIS A 288 
 PHE   0.014   0.001   PHE C  38 
 TYR   0.010   0.001   TYR A 251 
 ARG   0.001   0.000   ARG A 455 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03127 (  375)
  hydrogen bonds       : angle       4.16288 ( 1100)
  SS BOND              : bond        0.00241 (    4)
  SS BOND              : angle       0.70621 (    8)
  covalent geometry    : bond        0.00267 ( 7040)
  covalent geometry    : angle       0.57440 ( 9571)

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

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.654 
Fit side-chains
REVERT: A  170 GLN cc_start: 0.8233 (tp40) cc_final: 0.7842 (tp-100)
REVERT: A  263 LYS cc_start: 0.8312 (mmtt) cc_final: 0.7979 (mmpt)
REVERT: A  276 MET cc_start: 0.6487 (mmm) cc_final: 0.5908 (mmt)
REVERT: A  303 LEU cc_start: 0.8853 (mt) cc_final: 0.8629 (mp)
REVERT: B   91 LYS cc_start: 0.8256 (mttt) cc_final: 0.7962 (mtpt)
REVERT: B  105 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.6344 (tt0)
REVERT: B  155 SER cc_start: 0.8703 (p) cc_final: 0.8282 (t)
REVERT: B  200 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.6959 (pt)
REVERT: C   81 ILE cc_start: 0.8416 (mm) cc_final: 0.8106 (mm)
REVERT: C   95 TRP cc_start: 0.7777 (p-90) cc_final: 0.7462 (p-90)
  outliers start: 12
  outliers final: 10
  residues processed: 105
  average time/residue: 0.2062
  time to fit residues: 28.9150
Evaluate side-chains
  108 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.655 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain B residue    4 ILE
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain C residue   13 ARG
Chi-restraints excluded: chain C residue   90 THR
Chi-restraints excluded: chain C residue  137 LEU
Chi-restraints excluded: chain C residue  196 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 13 optimal weight:    0.0050
   chunk 54 optimal weight:    0.7980
   chunk 65 optimal weight:    4.9990
   chunk 31 optimal weight:    0.0060
   chunk 28 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9990
   chunk 22 optimal weight:    9.9990
   chunk 34 optimal weight:    0.6980
   chunk 51 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   chunk 3 optimal weight:    0.3980
   overall best weight:    0.3410

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

Flipped N/Q/H residues before XYZ refinement:
** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 420 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.174356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.136826 restraints weight = 23038.469|
|-----------------------------------------------------------------------------|
r_work (start): 0.3558 rms_B_bonded: 5.18
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3563
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3563 r_free = 0.3563    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3564 r_free = 0.3564    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3564
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7716
moved from start:          0.3150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7044  Z= 0.121
  Angle     :  0.576   7.474   9579  Z= 0.280
  Chirality :  0.039   0.153   1140
  Planarity :  0.005   0.065   1132
  Dihedral  :  9.622  59.633   1805
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 16.26 %
    Favored  : 81.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.30), residues: 865
  helix:  2.02 (0.26), residues: 385
  sheet: -0.85 (0.37), residues: 205
  loop : -2.33 (0.35), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 344 
 HIS   0.002   0.001   HIS A 288 
 PHE   0.015   0.001   PHE C  38 
 TYR   0.010   0.001   TYR A 251 
 ARG   0.001   0.000   ARG A 455 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03132 (  375)
  hydrogen bonds       : angle       4.13598 ( 1100)
  SS BOND              : bond        0.00252 (    4)
  SS BOND              : angle       0.70659 (    8)
  covalent geometry    : bond        0.00279 ( 7040)
  covalent geometry    : angle       0.57549 ( 9571)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4765.23 seconds
wall clock time: 85 minutes 38.91 seconds (5138.91 seconds total)