Starting phenix.real_space_refine
on Wed Mar 12 20:28:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d2x_27153/03_2025/8d2x_27153.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d2x_27153/03_2025/8d2x_27153.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8d2x_27153/03_2025/8d2x_27153.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d2x_27153/03_2025/8d2x_27153.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d2x_27153/03_2025/8d2x_27153.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d2x_27153/03_2025/8d2x_27153.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.044
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 1611 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      33      5.16       5
     C    4465      2.51       5
     N    1027      2.21       5
     O    1288      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6813
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3445
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 460, 3404
          Classifications: {'peptide': 460}
          Incomplete info: {'truncation_to_alanine': 55}
          Link IDs: {'PTRANS': 20, 'TRANS': 439}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 196
          Unresolved non-hydrogen angles: 233
          Unresolved non-hydrogen dihedrals: 163
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 107
      Conformer: "B"
        Number of residues, atoms: 460, 3404
          Classifications: {'peptide': 460}
          Incomplete info: {'truncation_to_alanine': 55}
          Link IDs: {'PTRANS': 20, 'TRANS': 439}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 196
          Unresolved non-hydrogen angles: 233
          Unresolved non-hydrogen dihedrals: 163
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 107
          bond proxies already assigned to first conformer: 3449
    Chain: "B"
      Number of atoms: 1401
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1401
          Classifications: {'peptide': 201}
          Incomplete info: {'truncation_to_alanine': 18}
          Link IDs: {'PTRANS': 14, 'TRANS': 186}
          Unresolved non-hydrogen bonds: 52
          Unresolved non-hydrogen angles: 64
          Unresolved non-hydrogen dihedrals: 40
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 5}
          Unresolved non-hydrogen planarities: 31
    Chain: "C"
      Number of atoms: 1416
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 203, 1405
          Classifications: {'peptide': 203}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 12, 'TRANS': 190}
          Unresolved non-hydrogen bonds: 48
          Unresolved non-hydrogen angles: 57
          Unresolved non-hydrogen dihedrals: 39
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 18
      Conformer: "B"
        Number of residues, atoms: 203, 1405
          Classifications: {'peptide': 203}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 12, 'TRANS': 190}
          Unresolved non-hydrogen bonds: 48
          Unresolved non-hydrogen angles: 57
          Unresolved non-hydrogen dihedrals: 39
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 18
          bond proxies already assigned to first conformer: 1433
    Chain: "A"
      Number of atoms: 551
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 18, 481
          Unusual residues: {'LMT': 13, 'ZGS': 1}
          Classifications: {'undetermined': 14, 'water': 4}
          Link IDs: {None: 17}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 16
          Unresolved non-hydrogen chiralities: 1
      Conformer: "B"
        Number of residues, atoms: 18, 481
          Unusual residues: {'LMT': 13, 'ZGS': 1}
          Classifications: {'undetermined': 14, 'water': 4}
          Link IDs: {None: 17}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 16
          Unresolved non-hydrogen chiralities: 1
          bond proxies already assigned to first conformer: 417
  Residues with excluded nonbonded symmetry interactions: 7
    residue:
      pdb=" N  AARG A  84 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A  84 " occ=0.50
    residue:
      pdb=" N  AMET A 181 " occ=0.50
      ... (14 atoms not shown)
      pdb=" CE BMET A 181 " occ=0.50
    residue:
      pdb=" N  APHE A 396 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE A 396 " occ=0.50
    residue:
      pdb=" N  APHE A 449 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE A 449 " occ=0.50
    residue:
      pdb=" N  AARG C  13 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG C  13 " occ=0.50
    residue:
      pdb=" C1 ALMT A 604 " occ=0.50
      ... (68 atoms not shown)
      pdb=" O6BBLMT A 604 " occ=0.50
    residue:
      pdb=" C1 ALMT A 613 " occ=0.50
      ... (68 atoms not shown)
      pdb=" O6BBLMT A 613 " occ=0.50
  Time building chain proxies: 8.05, per 1000 atoms: 1.18
  Number of scatterers: 6813
  At special positions: 0
  Unit cell: (70.896, 72.584, 141.792, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      33     16.00
     O    1288      8.00
     N    1027      7.00
     C    4465      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=2.04
    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=2.02
    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: 2.26
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1574

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 11 sheets defined
      46.8% alpha, 17.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.67
  Creating SS restraints...
    Processing helix  chain 'A' and resid 36 through 47
      removed outlier: 3.658A  pdb=" N   GLY A  47 " --> pdb=" O   TYR A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 60
      removed outlier: 3.997A  pdb=" N   GLN A  51 " --> pdb=" O   GLY A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 60 through 67
    Processing helix  chain 'A' and resid 72 through 100
      removed outlier: 3.654A  pdb=" N   ASP A  87 " --> pdb=" O   GLY A  83 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   ALA A  88 " --> pdb=" O  AARG A  84 " (cutoff:3.500A)
      Proline residue:  A  92  - end of helix
    Processing helix  chain 'A' and resid 109 through 128
      Proline residue:  A 118  - end of helix
      removed outlier: 3.519A  pdb=" N   LEU A 122 " --> pdb=" O   PRO A 118 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   TRP A 128 " --> pdb=" O   TYR A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 167
      removed outlier: 3.699A  pdb=" N   TRP A 140 " --> pdb=" O   GLY A 136 " (cutoff:3.500A)
      Proline residue:  A 158  - end of helix
      removed outlier: 3.527A  pdb=" N   ALA A 161 " --> pdb=" O   VAL A 157 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   THR A 163 " --> pdb=" O   TYR A 159 " (cutoff:3.500A)
      removed outlier: 4.660A  pdb=" N   MET A 164 " --> pdb=" O   SER A 160 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   SER A 167 " --> pdb=" O   THR A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 202
      removed outlier: 3.904A  pdb=" N   ALA A 202 " --> pdb=" O   ILE A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 213
    Processing helix  chain 'A' and resid 232 through 262
    Processing helix  chain 'A' and resid 277 through 288
      removed outlier: 3.521A  pdb=" N   HIS A 288 " --> pdb=" O   MET A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 311
    Processing helix  chain 'A' and resid 312 through 319
    Processing helix  chain 'A' and resid 325 through 340
      removed outlier: 3.537A  pdb=" N   VAL A 329 " --> pdb=" O   ASP A 325 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   LEU A 330 " --> pdb=" O   PHE A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 351
    Processing helix  chain 'A' and resid 353 through 361
      removed outlier: 4.089A  pdb=" N   THR A 361 " --> pdb=" O   VAL A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 373
      removed outlier: 4.333A  pdb=" N   PHE A 367 " --> pdb=" O   SER A 363 " (cutoff:3.500A)
      removed outlier: 4.023A  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
    Processing helix  chain 'A' and resid 460 through 473
      removed outlier: 3.663A  pdb=" N   LEU A 465 " --> pdb=" O   GLY A 461 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 488
      removed outlier: 3.594A  pdb=" N   SER A 488 " --> pdb=" O   LEU A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 493 through 507
      removed outlier: 3.939A  pdb=" N   GLN A 497 " --> pdb=" O   GLU A 493 " (cutoff:3.500A)
      removed outlier: 5.105A  pdb=" N   ASN A 499 " --> pdb=" O   LYS A 495 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 123
    Processing helix  chain 'C' and resid 28 through 31
    Processing sheet with id=AA1, first strand: chain 'B' and resid 11 through 12
      removed outlier: 5.942A  pdb=" N   LYS B  11 " --> pdb=" O   ASN B 102 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    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 52 through 53
      removed outlier: 6.419A  pdb=" N   TRP B  34 " --> pdb=" O   LEU B  46 " (cutoff:3.500A)
      removed outlier: 4.545A  pdb=" N   TYR B  48 " --> pdb=" O   VAL B  32 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   VAL B  32 " --> pdb=" O   TYR B  48 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 112 through 114
      removed outlier: 4.896A  pdb=" N   ALA B 127 " --> pdb=" O   ILE B 174 " (cutoff:3.500A)
      removed outlier: 7.220A  pdb=" N   ILE B 174 " --> pdb=" O   ALA B 127 " (cutoff:3.500A)
      removed outlier: 5.710A  pdb=" N   VAL B 129 " --> pdb=" O   LEU B 172 " (cutoff:3.500A)
      removed outlier: 7.322A  pdb=" N   LEU B 172 " --> pdb=" O   VAL B 129 " (cutoff:3.500A)
      removed outlier: 5.523A  pdb=" N   PHE B 131 " --> pdb=" O   ALA B 170 " (cutoff:3.500A)
      removed outlier: 7.096A  pdb=" N   ALA B 170 " --> pdb=" O   PHE B 131 " (cutoff:3.500A)
      removed outlier: 5.481A  pdb=" N   MET B 168 " --> pdb=" O   PRO B 133 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 140 through 144
    Processing sheet with id=AA6, first strand: chain 'C' and resid 3 through 6
      removed outlier: 3.544A  pdb=" N   ALA C  77 " --> pdb=" O   CYS C  22 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 56 through 58
      removed outlier: 5.203A  pdb=" N   TRP C  46 " --> pdb=" O   PHE C  38 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   PHE C  38 " --> pdb=" O   TRP C  46 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   ALA C  48 " --> pdb=" O   TRP C  36 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   TRP C  33 " --> pdb=" O   LYS C  96 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 89 through 91
    Processing sheet with id=AA9, first strand: chain 'C' and resid 121 through 123
      removed outlier: 5.867A  pdb=" N   TRP C 170 " --> pdb=" O   GLY C 143 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 121 through 123
      removed outlier: 5.867A  pdb=" N   TRP C 170 " --> pdb=" O   GLY C 143 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   LEU C 169 " --> pdb=" O   ASN C 166 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 184 through 187
      removed outlier: 4.726A  pdb=" N   ALA C 184 " --> pdb=" O   VAL C 200 " (cutoff:3.500A)

    384 hydrogen bonds defined for protein.
    1087 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.87

  Time building geometry restraints manager: 2.45 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 990
        1.31 -     1.44: 1961
        1.44 -     1.56: 3948
        1.56 -     1.69: 55
        1.69 -     1.81: 46
  Bond restraints: 7000
  Sorted by residual:
  bond pdb=" C1B LMT A 612 "
       pdb=" O5B LMT A 612 "
    ideal  model  delta    sigma   weight residual
    1.393  1.523 -0.130 2.00e-02 2.50e+03 4.21e+01
  bond pdb=" C1B LMT A 610 "
       pdb=" O5B LMT A 610 "
    ideal  model  delta    sigma   weight residual
    1.393  1.521 -0.128 2.00e-02 2.50e+03 4.09e+01
  bond pdb=" C1B LMT A 608 "
       pdb=" O5B LMT A 608 "
    ideal  model  delta    sigma   weight residual
    1.393  1.520 -0.127 2.00e-02 2.50e+03 4.03e+01
  bond pdb=" C1BALMT A 613 "
       pdb=" O5BALMT A 613 "
    ideal  model  delta    sigma   weight residual
    1.393  1.518 -0.125 2.00e-02 2.50e+03 3.91e+01
  bond pdb=" C1B LMT A 609 "
       pdb=" O5B LMT A 609 "
    ideal  model  delta    sigma   weight residual
    1.393  1.517 -0.124 2.00e-02 2.50e+03 3.83e+01
  ... (remaining 6995 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.99: 9337
        4.99 -     9.98: 204
        9.98 -    14.96: 0
       14.96 -    19.95: 4
       19.95 -    24.94: 3
  Bond angle restraints: 9548
  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  152.10  -24.94 3.00e+00 1.11e-01 6.91e+01
  angle pdb=" C06 ZGS A 601 "
        pdb=" C07 ZGS A 601 "
        pdb=" C08 ZGS A 601 "
      ideal   model   delta    sigma   weight residual
     127.52  152.20  -24.68 3.00e+00 1.11e-01 6.77e+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  151.48  -24.14 3.00e+00 1.11e-01 6.47e+01
  angle pdb=" C04 ZGS A 601 "
        pdb=" C05 ZGS A 601 "
        pdb=" C06 ZGS A 601 "
      ideal   model   delta    sigma   weight residual
     110.70  130.46  -19.76 3.00e+00 1.11e-01 4.34e+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  110.53   17.14 3.00e+00 1.11e-01 3.26e+01
  ... (remaining 9543 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.22: 4009
       23.22 -    46.44: 286
       46.44 -    69.66: 111
       69.66 -    92.88: 72
       92.88 -   116.10: 135
  Dihedral angle restraints: 4613
    sinusoidal: 2141
      harmonic: 2472
  Sorted by residual:
  dihedral pdb=" C1' LMT A 608 "
           pdb=" C2' LMT A 608 "
           pdb=" C3' LMT A 608 "
           pdb=" O3' LMT A 608 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -176.68  -60.58 -116.10     1      3.00e+01 1.11e-03 1.54e+01
  dihedral pdb=" C2B LMT A 611 "
           pdb=" C1B LMT A 611 "
           pdb=" O5B LMT A 611 "
           pdb=" C5B LMT A 611 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -57.12   58.43 -115.55     1      3.00e+01 1.11e-03 1.53e+01
  dihedral pdb=" C5B LMT A 611 "
           pdb=" C1B LMT A 611 "
           pdb=" O5B LMT A 611 "
           pdb=" O1B LMT A 611 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -64.39 -179.76  115.37     1      3.00e+01 1.11e-03 1.52e+01
  ... (remaining 4610 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 837
       0.053 -    0.107: 230
       0.107 -    0.160: 73
       0.160 -    0.213: 7
       0.213 -    0.266: 8
  Chirality restraints: 1155
  Sorted by residual:
  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   -2.47    0.27 2.00e-01 2.50e+01 1.77e+00
  chirality pdb=" C4' LMT A 614 "
            pdb=" C3' LMT A 614 "
            pdb=" C5' LMT A 614 "
            pdb=" O1B LMT A 614 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.55   -2.29   -0.26 2.00e-01 2.50e+01 1.68e+00
  chirality pdb=" C1B LMT A 607 "
            pdb=" C2B LMT A 607 "
            pdb=" O1B LMT A 607 "
            pdb=" O5B LMT A 607 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.20   -2.45    0.25 2.00e-01 2.50e+01 1.52e+00
  ... (remaining 1152 not shown)

  Planarity restraints: 1135
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 204 "    0.015 2.00e-02 2.50e+03   3.06e-02 9.34e+00
        pdb=" C   ALA A 204 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   ALA A 204 "    0.020 2.00e-02 2.50e+03
        pdb=" N   PRO A 205 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP C  46 "   -0.036 5.00e-02 4.00e+02   5.39e-02 4.64e+00
        pdb=" N   PRO C  47 "    0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO C  47 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO C  47 "   -0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B  75 "   -0.034 5.00e-02 4.00e+02   5.12e-02 4.20e+00
        pdb=" N   PRO B  76 "    0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO B  76 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO B  76 "   -0.029 5.00e-02 4.00e+02
  ... (remaining 1132 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1540
        2.79 -     3.32: 5980
        3.32 -     3.84: 11561
        3.84 -     4.37: 12568
        4.37 -     4.90: 22716
  Nonbonded interactions: 54365
  Sorted by model distance:
  nonbonded pdb=" O   TYR A  43 "
            pdb=" OH  TYR A 159 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" OG1 THR A  53 "
            pdb=" OE1 GLN A 152 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" OD1 ASP A  67 "
            pdb=" OH  TYR A 452 "
     model   vdw
     2.308 3.040
  nonbonded pdb=" O   SER B  30 "
            pdb=" OG  SER B  30 "
     model   vdw
     2.343 3.040
  nonbonded pdb=" O   THR A 381 "
            pdb=" OG  SER A 385 "
     model   vdw
     2.344 3.040
  ... (remaining 54360 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=0.98
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             132.060
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     24.490
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  159.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
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   0.130   7000  Z= 0.794
  Angle     :  1.402  24.938   9548  Z= 0.568
  Chirality :  0.057   0.266   1155
  Planarity :  0.007   0.054   1135
  Dihedral  : 30.539 116.099   3027
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.66 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  6.42 %
    Favored  : 93.24 %
  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: -1.77 (0.26), residues: 871
  helix:  0.18 (0.24), residues: 390
  sheet: -0.79 (0.40), residues: 162
  loop : -3.13 (0.28), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C 106 
 HIS   0.002   0.001   HIS A 156 
 PHE   0.021   0.002   PHE B  89 
 TYR   0.016   0.001   TYR B  48 
 ARG   0.002   0.000   ARG A 323 

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

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

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 157
  time to evaluate  : 0.793 
Fit side-chains
REVERT: A   70 LEU cc_start: 0.8582 (mt) cc_final: 0.8381 (mt)
REVERT: A  134 ASP cc_start: 0.7768 (m-30) cc_final: 0.7261 (p0)
  outliers start: 1
  outliers final: 0
  residues processed: 157
  average time/residue: 0.1910
  time to fit residues: 39.7397
Evaluate side-chains
  117 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 65 optimal weight:    7.9990
   chunk 36 optimal weight:    0.9990
   chunk 22 optimal weight:   50.0000
   chunk 43 optimal weight:    0.8980
   chunk 34 optimal weight:    0.5980
   chunk 67 optimal weight:    0.1980
   chunk 26 optimal weight:    0.5980
   chunk 40 optimal weight:    0.5980
   chunk 50 optimal weight:    0.1980
   chunk 78 optimal weight:    0.9990
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
A 324 ASN
B  23 ASN
C  39 GLN
C  57 GLN
C 171 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.172418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.146096 restraints weight = 50130.538|
|-----------------------------------------------------------------------------|
r_work (start): 0.3693 rms_B_bonded: 5.85
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3693
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3693 r_free = 0.3693    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3692 r_free = 0.3692    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3692
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.2086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   7000  Z= 0.244
  Angle     :  0.912   9.630   9548  Z= 0.385
  Chirality :  0.055   0.554   1155
  Planarity :  0.005   0.055   1135
  Dihedral  : 17.902  70.056   1851
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.96 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 13.18 %
    Favored  : 83.45 %
  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: -0.84 (0.28), residues: 871
  helix:  1.34 (0.25), residues: 382
  sheet: -0.63 (0.42), residues: 162
  loop : -2.95 (0.29), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 103 
 HIS   0.008   0.002   HIS A 288 
 PHE   0.014   0.002   PHE A 367 
 TYR   0.014   0.001   TYR A 251 
 ARG   0.005   0.001   ARG A 108 

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

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

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 123
  time to evaluate  : 0.633 
Fit side-chains
   revert: symmetry clash
REVERT: A   70 LEU cc_start: 0.8717 (mt) cc_final: 0.8487 (mt)
REVERT: A  134 ASP cc_start: 0.7324 (m-30) cc_final: 0.6976 (p0)
REVERT: A  291 TYR cc_start: 0.7150 (OUTLIER) cc_final: 0.6117 (t80)
REVERT: C  190 PHE cc_start: 0.7798 (t80) cc_final: 0.7285 (t80)
  outliers start: 19
  outliers final: 10
  residues processed: 135
  average time/residue: 0.1769
  time to fit residues: 31.8744
Evaluate side-chains
  118 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 107
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain B residue    4 ILE
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  175 THR
Chi-restraints excluded: chain C residue  194 THR
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 67 optimal weight:    0.0570
   chunk 11 optimal weight:    0.9980
   chunk 85 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 49 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9990
   chunk 14 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 72 optimal weight:    0.5980
   chunk 22 optimal weight:    8.9990
   overall best weight:    0.5298

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

Flipped N/Q/H residues before XYZ refinement:
** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  23 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.171222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.145778 restraints weight = 48388.382|
|-----------------------------------------------------------------------------|
r_work (start): 0.3681 rms_B_bonded: 5.06
r_work (final): 0.3681
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3681
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3681 r_free = 0.3681    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3681 r_free = 0.3681    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3681
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.2323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   7000  Z= 0.232
  Angle     :  0.772   9.226   9548  Z= 0.342
  Chirality :  0.048   0.310   1155
  Planarity :  0.005   0.052   1135
  Dihedral  : 12.443  59.293   1851
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.31 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 16.89 %
    Favored  : 80.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (0.29), residues: 871
  helix:  1.79 (0.26), residues: 385
  sheet: -0.77 (0.41), residues: 167
  loop : -2.82 (0.30), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 346 
 HIS   0.002   0.001   HIS A 156 
 PHE   0.017   0.002   PHE A 427 
 TYR   0.015   0.001   TYR A 251 
 ARG   0.004   0.001   ARG B 191 

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

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

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 117
  time to evaluate  : 0.621 
Fit side-chains
REVERT: A   70 LEU cc_start: 0.8728 (mt) cc_final: 0.8499 (mt)
REVERT: A  134 ASP cc_start: 0.7214 (m-30) cc_final: 0.6912 (p0)
REVERT: A  170 GLN cc_start: 0.7128 (tp40) cc_final: 0.6879 (tp40)
REVERT: A  291 TYR cc_start: 0.7011 (OUTLIER) cc_final: 0.6152 (t80)
  outliers start: 17
  outliers final: 11
  residues processed: 124
  average time/residue: 0.1981
  time to fit residues: 32.5915
Evaluate side-chains
  119 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 107
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  302 SER
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain B residue    4 ILE
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain C residue  194 THR
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 26 optimal weight:    0.7980
   chunk 42 optimal weight:    0.7980
   chunk 63 optimal weight:    0.5980
   chunk 62 optimal weight:    1.9990
   chunk 7 optimal weight:    4.9990
   chunk 3 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   chunk 59 optimal weight:    0.0980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 324 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.170784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.144222 restraints weight = 59640.823|
|-----------------------------------------------------------------------------|
r_work (start): 0.3651 rms_B_bonded: 5.77
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3652
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3652 r_free = 0.3652    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3652 r_free = 0.3652    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3652
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
moved from start:          0.2518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7000  Z= 0.237
  Angle     :  0.726  10.066   9548  Z= 0.330
  Chirality :  0.045   0.289   1155
  Planarity :  0.005   0.058   1135
  Dihedral  : 11.190  59.178   1851
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 18.24 %
    Favored  : 78.55 %
  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: -0.40 (0.29), residues: 871
  helix:  1.89 (0.26), residues: 385
  sheet: -0.88 (0.39), residues: 177
  loop : -2.80 (0.31), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 346 
 HIS   0.002   0.001   HIS A 156 
 PHE   0.016   0.002   PHE B  89 
 TYR   0.015   0.001   TYR A 251 
 ARG   0.004   0.001   ARG B 191 

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

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

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 111
  time to evaluate  : 0.645 
Fit side-chains
REVERT: A   70 LEU cc_start: 0.8735 (mt) cc_final: 0.8516 (mt)
REVERT: A  134 ASP cc_start: 0.7204 (m-30) cc_final: 0.6842 (p0)
REVERT: A  291 TYR cc_start: 0.7139 (OUTLIER) cc_final: 0.6158 (t80)
REVERT: A  325 ASP cc_start: 0.7276 (p0) cc_final: 0.7061 (p0)
  outliers start: 18
  outliers final: 12
  residues processed: 121
  average time/residue: 0.1856
  time to fit residues: 29.8870
Evaluate side-chains
  120 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 107
  time to evaluate  : 0.620 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain B residue    4 ILE
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  194 THR
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 19 optimal weight:    1.9990
   chunk 57 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9980
   chunk 12 optimal weight:    0.3980
   chunk 41 optimal weight:    0.1980
   chunk 39 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 40 optimal weight:    0.4980
   chunk 75 optimal weight:    0.2980
   overall best weight:    0.4580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.171338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.145297 restraints weight = 53302.993|
|-----------------------------------------------------------------------------|
r_work (start): 0.3675 rms_B_bonded: 5.60
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3676
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3676 r_free = 0.3676    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3675 r_free = 0.3675    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3675
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7695
moved from start:          0.2686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7000  Z= 0.213
  Angle     :  0.698   9.600   9548  Z= 0.319
  Chirality :  0.043   0.275   1155
  Planarity :  0.005   0.057   1135
  Dihedral  : 10.567  59.145   1851
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 18.75 %
    Favored  : 78.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (0.29), residues: 871
  helix:  1.98 (0.26), residues: 385
  sheet: -0.90 (0.39), residues: 177
  loop : -2.69 (0.32), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 346 
 HIS   0.002   0.001   HIS A 288 
 PHE   0.025   0.002   PHE A 367 
 TYR   0.016   0.001   TYR C 123 
 ARG   0.004   0.001   ARG B 104 

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

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

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 0.651 
Fit side-chains
REVERT: A   70 LEU cc_start: 0.8716 (mt) cc_final: 0.8481 (mt)
REVERT: A  288 HIS cc_start: 0.6307 (t-170) cc_final: 0.6073 (t-90)
REVERT: A  291 TYR cc_start: 0.7194 (OUTLIER) cc_final: 0.6301 (t80)
REVERT: C  190 PHE cc_start: 0.7772 (t80) cc_final: 0.7314 (t80)
  outliers start: 17
  outliers final: 11
  residues processed: 124
  average time/residue: 0.1897
  time to fit residues: 31.4259
Evaluate side-chains
  119 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 107
  time to evaluate  : 0.624 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  244 SER
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain B residue    4 ILE
Chi-restraints excluded: chain B residue  172 LEU
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  194 THR
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 17 optimal weight:    0.8980
   chunk 85 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 76 optimal weight:    0.3980
   chunk 44 optimal weight:    4.9990
   chunk 59 optimal weight:    0.8980
   chunk 77 optimal weight:    0.0060
   chunk 32 optimal weight:    0.8980
   overall best weight:    0.6196

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.169934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.143085 restraints weight = 58218.961|
|-----------------------------------------------------------------------------|
r_work (start): 0.3641 rms_B_bonded: 6.07
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3642
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3642 r_free = 0.3642    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3642 r_free = 0.3642    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3642
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.2797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7000  Z= 0.251
  Angle     :  0.710   9.537   9548  Z= 0.329
  Chirality :  0.043   0.270   1155
  Planarity :  0.005   0.056   1135
  Dihedral  : 10.375  58.608   1851
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.31 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 19.09 %
    Favored  : 78.04 %
  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: 871
  helix:  1.89 (0.26), residues: 385
  sheet: -0.83 (0.41), residues: 162
  loop : -2.65 (0.31), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 346 
 HIS   0.002   0.001   HIS A 156 
 PHE   0.016   0.002   PHE C  38 
 TYR   0.025   0.002   TYR C 123 
 ARG   0.004   0.001   ARG B 104 

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

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

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 117
  time to evaluate  : 0.695 
Fit side-chains
REVERT: A  134 ASP cc_start: 0.7372 (m-30) cc_final: 0.7053 (p0)
REVERT: A  291 TYR cc_start: 0.7151 (OUTLIER) cc_final: 0.6219 (t80)
REVERT: A  325 ASP cc_start: 0.7429 (p0) cc_final: 0.7192 (p0)
REVERT: C  190 PHE cc_start: 0.7717 (t80) cc_final: 0.7213 (t80)
  outliers start: 16
  outliers final: 12
  residues processed: 127
  average time/residue: 0.1986
  time to fit residues: 33.5202
Evaluate side-chains
  128 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 115
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  244 SER
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  429 VAL
Chi-restraints excluded: chain A residue  471 VAL
Chi-restraints excluded: chain B residue    4 ILE
Chi-restraints excluded: chain B residue  172 LEU
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  194 THR
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 9 optimal weight:    0.7980
   chunk 47 optimal weight:    0.0470
   chunk 67 optimal weight:    0.0770
   chunk 59 optimal weight:    0.7980
   chunk 3 optimal weight:    0.1980
   chunk 50 optimal weight:    0.7980
   chunk 61 optimal weight:    0.2980
   chunk 48 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 16 optimal weight:    0.6980
   chunk 75 optimal weight:    0.2980
   overall best weight:    0.1836

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

Flipped N/Q/H residues before XYZ refinement:
A 311 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.174402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.147857 restraints weight = 52128.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.3698 rms_B_bonded: 6.03
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3698
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3698 r_free = 0.3698    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3698 r_free = 0.3698    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3698
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.2912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7000  Z= 0.163
  Angle     :  0.669   9.656   9548  Z= 0.309
  Chirality :  0.042   0.273   1155
  Planarity :  0.005   0.056   1135
  Dihedral  : 10.015  56.975   1851
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 19.26 %
    Favored  : 78.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.19 (0.29), residues: 871
  helix:  2.00 (0.26), residues: 387
  sheet: -0.83 (0.39), residues: 172
  loop : -2.56 (0.33), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP A 346 
 HIS   0.002   0.001   HIS A 288 
 PHE   0.033   0.001   PHE A 367 
 TYR   0.010   0.001   TYR A 251 
 ARG   0.007   0.001   ARG B 191 

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

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

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 116
  time to evaluate  : 0.636 
Fit side-chains
REVERT: A  291 TYR cc_start: 0.7126 (OUTLIER) cc_final: 0.6327 (t80)
REVERT: C  190 PHE cc_start: 0.7639 (t80) cc_final: 0.7384 (t80)
  outliers start: 13
  outliers final: 10
  residues processed: 121
  average time/residue: 0.2030
  time to fit residues: 32.3005
Evaluate side-chains
  118 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 107
  time to evaluate  : 0.639 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 CYS
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain B residue    4 ILE
Chi-restraints excluded: chain B residue   71 MET
Chi-restraints excluded: chain B residue  172 LEU
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  194 THR
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 9 optimal weight:    0.9990
   chunk 34 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9980
   chunk 52 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0370
   chunk 65 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9980
   chunk 35 optimal weight:    0.5980
   chunk 53 optimal weight:    0.8980
   chunk 68 optimal weight:    0.0980
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.4458

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

Flipped N/Q/H residues before XYZ refinement:
A 324 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.171748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.145753 restraints weight = 51189.279|
|-----------------------------------------------------------------------------|
r_work (start): 0.3684 rms_B_bonded: 5.42
r_work (final): 0.3684
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3685
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3685 r_free = 0.3685    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3684 r_free = 0.3684    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3684
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.2985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7000  Z= 0.213
  Angle     :  0.686   9.455   9548  Z= 0.318
  Chirality :  0.043   0.271   1155
  Planarity :  0.005   0.064   1135
  Dihedral  :  9.951  59.924   1851
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.19 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 19.59 %
    Favored  : 78.04 %
  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: 871
  helix:  2.03 (0.26), residues: 386
  sheet: -0.88 (0.39), residues: 171
  loop : -2.49 (0.33), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 346 
 HIS   0.004   0.001   HIS A 288 
 PHE   0.018   0.001   PHE A 386 
 TYR   0.014   0.001   TYR A 251 
 ARG   0.004   0.001   ARG A 108 

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

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

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 112
  time to evaluate  : 0.705 
Fit side-chains
REVERT: A  291 TYR cc_start: 0.7315 (OUTLIER) cc_final: 0.5885 (t80)
REVERT: C  190 PHE cc_start: 0.7665 (t80) cc_final: 0.7322 (t80)
  outliers start: 13
  outliers final: 11
  residues processed: 119
  average time/residue: 0.1943
  time to fit residues: 30.8355
Evaluate side-chains
  123 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 111
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 CYS
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain B residue    4 ILE
Chi-restraints excluded: chain B residue   71 MET
Chi-restraints excluded: chain B residue  172 LEU
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  194 THR
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 29 optimal weight:    0.8980
   chunk 12 optimal weight:    0.4980
   chunk 67 optimal weight:    0.9990
   chunk 43 optimal weight:    0.6980
   chunk 40 optimal weight:    0.0770
   chunk 74 optimal weight:    4.9990
   chunk 47 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 56 optimal weight:    0.0370
   chunk 37 optimal weight:    3.9990
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.4216

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

Flipped N/Q/H residues before XYZ refinement:
A 324 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.172185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.147922 restraints weight = 44636.469|
|-----------------------------------------------------------------------------|
r_work (start): 0.3718 rms_B_bonded: 4.56
r_work (final): 0.3718
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3717
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3717 r_free = 0.3717    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3717 r_free = 0.3717    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3717
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.3028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7000  Z= 0.204
  Angle     :  0.677   9.325   9548  Z= 0.315
  Chirality :  0.042   0.271   1155
  Planarity :  0.005   0.064   1135
  Dihedral  :  9.873  58.962   1851
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 19.43 %
    Favored  : 78.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.29), residues: 871
  helix:  2.06 (0.26), residues: 385
  sheet: -0.73 (0.40), residues: 166
  loop : -2.49 (0.33), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 346 
 HIS   0.002   0.001   HIS A 156 
 PHE   0.014   0.001   PHE C  38 
 TYR   0.015   0.001   TYR C 123 
 ARG   0.004   0.001   ARG A 173 

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

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

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 110
  time to evaluate  : 0.715 
Fit side-chains
   revert: symmetry clash
REVERT: A  291 TYR cc_start: 0.7275 (OUTLIER) cc_final: 0.5981 (t80)
REVERT: C  190 PHE cc_start: 0.7633 (t80) cc_final: 0.7353 (t80)
  outliers start: 14
  outliers final: 12
  residues processed: 117
  average time/residue: 0.1974
  time to fit residues: 30.7217
Evaluate side-chains
  122 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 109
  time to evaluate  : 0.730 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 CYS
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  244 SER
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain B residue    4 ILE
Chi-restraints excluded: chain B residue   71 MET
Chi-restraints excluded: chain B residue  172 LEU
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  194 THR
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 83 optimal weight:    2.9990
   chunk 44 optimal weight:    0.6980
   chunk 54 optimal weight:    0.2980
   chunk 56 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 39 optimal weight:    0.6980
   chunk 26 optimal weight:    0.4980
   chunk 31 optimal weight:    0.0020
   chunk 60 optimal weight:    1.9990
   overall best weight:    0.4388

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

Flipped N/Q/H residues before XYZ refinement:
A 324 ASN
** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.171850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.145490 restraints weight = 47912.232|
|-----------------------------------------------------------------------------|
r_work (start): 0.3688 rms_B_bonded: 5.62
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3688
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3688 r_free = 0.3688    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3688 r_free = 0.3688    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3688
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.3119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7000  Z= 0.211
  Angle     :  0.692   9.298   9548  Z= 0.321
  Chirality :  0.043   0.271   1155
  Planarity :  0.005   0.064   1135
  Dihedral  :  9.826  59.983   1851
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 19.76 %
    Favored  : 78.04 %
  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: -0.13 (0.30), residues: 871
  helix:  2.00 (0.27), residues: 386
  sheet: -0.73 (0.40), residues: 166
  loop : -2.45 (0.33), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 346 
 HIS   0.003   0.001   HIS A 288 
 PHE   0.028   0.001   PHE A 367 
 TYR   0.015   0.001   TYR C 123 
 ARG   0.007   0.001   ARG A 173 

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

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

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 0.694 
Fit side-chains
REVERT: A  291 TYR cc_start: 0.7191 (OUTLIER) cc_final: 0.5824 (t80)
REVERT: C  190 PHE cc_start: 0.7659 (t80) cc_final: 0.7385 (t80)
  outliers start: 12
  outliers final: 11
  residues processed: 116
  average time/residue: 0.2031
  time to fit residues: 31.1870
Evaluate side-chains
  120 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 108
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 CYS
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  244 SER
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain B residue    4 ILE
Chi-restraints excluded: chain B residue   71 MET
Chi-restraints excluded: chain B residue  172 LEU
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  194 THR
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 78 optimal weight:    0.9980
   chunk 69 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 85 optimal weight:    0.0050
   chunk 64 optimal weight:    6.9990
   chunk 59 optimal weight:    0.3980
   chunk 70 optimal weight:    0.2980
   chunk 49 optimal weight:    0.6980
   chunk 56 optimal weight:    0.0570
   chunk 80 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   overall best weight:    0.2912

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

Flipped N/Q/H residues before XYZ refinement:
** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 324 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.172930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.146116 restraints weight = 53264.583|
|-----------------------------------------------------------------------------|
r_work (start): 0.3690 rms_B_bonded: 6.08
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3691
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3691 r_free = 0.3691    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3691 r_free = 0.3691    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3691
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.3148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7000  Z= 0.181
  Angle     :  0.674   9.104   9548  Z= 0.315
  Chirality :  0.042   0.272   1155
  Planarity :  0.005   0.062   1135
  Dihedral  :  9.693  59.815   1851
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 19.59 %
    Favored  : 78.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.30), residues: 871
  helix:  2.02 (0.27), residues: 386
  sheet: -0.71 (0.40), residues: 166
  loop : -2.43 (0.34), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP A 346 
 HIS   0.001   0.000   HIS A 156 
 PHE   0.025   0.001   PHE A 367 
 TYR   0.015   0.001   TYR C 123 
 ARG   0.008   0.001   ARG A 173 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3184.90 seconds
wall clock time: 56 minutes 0.04 seconds (3360.04 seconds total)