Starting phenix.real_space_refine
on Wed Feb 12 21:11:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d2w_27152/02_2025/8d2w_27152.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d2w_27152/02_2025/8d2w_27152.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8d2w_27152/02_2025/8d2w_27152.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d2w_27152/02_2025/8d2w_27152.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d2w_27152/02_2025/8d2w_27152.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d2w_27152/02_2025/8d2w_27152.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.045
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1622 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      34      5.16       5
     C    4501      2.51       5
     N    1026      2.21       5
     O    1296      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6858
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3442
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 460, 3417
          Classifications: {'peptide': 460}
          Incomplete info: {'truncation_to_alanine': 49}
          Link IDs: {'PTRANS': 20, 'TRANS': 439}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 186
          Unresolved non-hydrogen angles: 224
          Unresolved non-hydrogen dihedrals: 157
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 115
      Conformer: "B"
        Number of residues, atoms: 460, 3417
          Classifications: {'peptide': 460}
          Incomplete info: {'truncation_to_alanine': 49}
          Link IDs: {'PTRANS': 20, 'TRANS': 439}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 186
          Unresolved non-hydrogen angles: 224
          Unresolved non-hydrogen dihedrals: 157
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 115
          bond proxies already assigned to first conformer: 3476
    Chain: "B"
      Number of atoms: 1404
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 201, 1393
          Classifications: {'peptide': 201}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 14, 'TRANS': 186}
          Unresolved non-hydrogen bonds: 60
          Unresolved non-hydrogen angles: 71
          Unresolved non-hydrogen dihedrals: 49
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 31
      Conformer: "B"
        Number of residues, atoms: 201, 1393
          Classifications: {'peptide': 201}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 14, 'TRANS': 186}
          Unresolved non-hydrogen bonds: 60
          Unresolved non-hydrogen angles: 71
          Unresolved non-hydrogen dihedrals: 49
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 31
          bond proxies already assigned to first conformer: 1419
    Chain: "C"
      Number of atoms: 1419
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 203, 1408
          Classifications: {'peptide': 203}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 12, 'TRANS': 190}
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 53
          Unresolved non-hydrogen dihedrals: 37
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 20
      Conformer: "B"
        Number of residues, atoms: 203, 1408
          Classifications: {'peptide': 203}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 12, 'TRANS': 190}
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 53
          Unresolved non-hydrogen dihedrals: 37
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 20
          bond proxies already assigned to first conformer: 1436
    Chain: "A"
      Number of atoms: 553
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 15, 448
          Unusual residues: {'LMT': 14, 'ZGS': 1}
          Classifications: {'undetermined': 15}
          Link IDs: {None: 14}
          Unresolved non-hydrogen bonds: 84
          Unresolved non-hydrogen angles: 126
          Unresolved non-hydrogen dihedrals: 179
          Unresolved non-hydrogen chiralities: 35
      Conformer: "B"
        Number of residues, atoms: 15, 448
          Unusual residues: {'LMT': 14, 'ZGS': 1}
          Classifications: {'undetermined': 15}
          Link IDs: {None: 14}
          Unresolved non-hydrogen bonds: 84
          Unresolved non-hydrogen angles: 126
          Unresolved non-hydrogen dihedrals: 179
          Unresolved non-hydrogen chiralities: 35
          bond proxies already assigned to first conformer: 346
    Chain: "C"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 35
          Unusual residues: {'LMT': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 5
          Classifications: {'water': 5}
          Link IDs: {None: 4}
  Residues with excluded nonbonded symmetry interactions: 7
    residue:
      pdb=" N  ATRP A 346 " occ=0.50
      ... (26 atoms not shown)
      pdb=" CH2BTRP A 346 " occ=0.50
    residue:
      pdb=" N  APHE A 449 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE A 449 " occ=0.50
    residue:
      pdb=" N  AARG B 191 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG B 191 " occ=0.50
    residue:
      pdb=" N  AARG C  13 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG C  13 " occ=0.50
    residue:
      pdb=" C1 ALMT A 602 " occ=0.50
      ... (68 atoms not shown)
      pdb=" O6BBLMT A 602 " occ=0.50
    residue:
      pdb=" C1 ALMT A 603 " occ=0.50
      ... (68 atoms not shown)
      pdb=" O6BBLMT A 603 " occ=0.50
    residue:
      pdb=" C1 ALMT A 610 " occ=0.50
      ... (68 atoms not shown)
      pdb=" O6BBLMT A 610 " occ=0.50
  Time building chain proxies: 4.48, per 1000 atoms: 0.65
  Number of scatterers: 6858
  At special positions: 0
  Unit cell: (69.208, 73.428, 141.792, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      34     16.00
     P       1     15.00
     O    1296      8.00
     N    1026      7.00
     C    4501      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  86 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 130 " - pdb=" SG  CYS B 186 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  93 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 139 " - pdb=" SG  CYS C 186 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.10
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 10 sheets defined
      45.5% alpha, 17.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.71
  Creating SS restraints...
    Processing helix  chain 'A' and resid 36 through 46
    Processing helix  chain 'A' and resid 47 through 67
      removed outlier: 3.998A  pdb=" N   GLN A  51 " --> pdb=" O   GLY A  47 " (cutoff:3.500A)
      removed outlier: 6.143A  pdb=" N   GLN A  62 " --> pdb=" O   GLY A  58 " (cutoff:3.500A)
      removed outlier: 5.286A  pdb=" N   ILE A  63 " --> pdb=" O   PHE A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 100
      removed outlier: 4.021A  pdb=" N   ALA A  88 " --> pdb=" O   ARG A  84 " (cutoff:3.500A)
      Proline residue:  A  92  - end of helix
    Processing helix  chain 'A' and resid 109 through 128
      Proline residue:  A 118  - end of helix
      removed outlier: 3.715A  pdb=" N   TRP A 128 " --> pdb=" O   TYR A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 162
      Proline residue:  A 158  - end of helix
    Processing helix  chain 'A' and resid 163 through 165
      No H-bonds generated for 'chain 'A' and resid 163 through 165'
    Processing helix  chain 'A' and resid 169 through 200
    Processing helix  chain 'A' and resid 232 through 262
      removed outlier: 3.512A  pdb=" N   VAL A 262 " --> pdb=" O   LEU A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 288
    Processing helix  chain 'A' and resid 288 through 311
    Processing helix  chain 'A' and resid 312 through 319
    Processing helix  chain 'A' and resid 325 through 352
      Proline residue:  A 342  - end of helix
      removed outlier: 3.770A  pdb=" N   THR A 349 " --> pdb=" O   GLN A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 371
      removed outlier: 3.664A  pdb=" N   THR A 361 " --> pdb=" O   VAL A 357 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   VAL A 364 " --> pdb=" O   GLY A 360 " (cutoff:3.500A)
      removed outlier: 4.550A  pdb=" N   VAL A 365 " --> pdb=" O   THR A 361 " (cutoff:3.500A)
      Proline residue:  A 366  - end of helix
    Processing helix  chain 'A' and resid 377 through 414
      removed outlier: 3.535A  pdb=" N   TYR A 382 " --> pdb=" O   LEU A 378 " (cutoff:3.500A)
      Proline residue:  A 399  - end of helix
      Proline residue:  A 404  - end of helix
    Processing helix  chain 'A' and resid 419 through 451
      removed outlier: 3.542A  pdb=" N   TYR A 425 " --> pdb=" O   GLU A 421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 473
      removed outlier: 3.574A  pdb=" N   LEU A 465 " --> pdb=" O   GLY A 461 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 488
      removed outlier: 3.570A  pdb=" N   SER A 488 " --> pdb=" O   LEU A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 493 through 507
      removed outlier: 3.644A  pdb=" N   GLN A 497 " --> pdb=" O   GLU A 493 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   GLY A 498 " --> pdb=" O   GLU A 494 " (cutoff:3.500A)
      removed outlier: 5.522A  pdb=" N   ASN A 499 " --> pdb=" O   LYS A 495 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 123
    Processing helix  chain 'C' and resid 28 through 31
    Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 5
    Processing sheet with id=AA2, first strand: chain 'B' and resid 11 through 12
      removed outlier: 5.976A  pdb=" N   LYS B  11 " --> pdb=" O   ASN B 102 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   VAL B  32 " --> pdb=" O   TYR B  48 " (cutoff:3.500A)
      removed outlier: 4.582A  pdb=" N   TYR B  48 " --> pdb=" O   VAL B  32 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   TRP B  34 " --> pdb=" O   LEU B  46 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 112 through 114
      removed outlier: 4.858A  pdb=" N   ALA B 127 " --> pdb=" O   ILE B 174 " (cutoff:3.500A)
      removed outlier: 7.185A  pdb=" N   ILE B 174 " --> pdb=" O   ALA B 127 " (cutoff:3.500A)
      removed outlier: 5.666A  pdb=" N   VAL B 129 " --> pdb=" O   LEU B 172 " (cutoff:3.500A)
      removed outlier: 7.304A  pdb=" N   LEU B 172 " --> pdb=" O   VAL B 129 " (cutoff:3.500A)
      removed outlier: 5.534A  pdb=" N   PHE B 131 " --> pdb=" O   ALA B 170 " (cutoff:3.500A)
      removed outlier: 7.166A  pdb=" N   ALA B 170 " --> pdb=" O   PHE B 131 " (cutoff:3.500A)
      removed outlier: 5.434A  pdb=" N   MET B 168 " --> pdb=" O   PRO B 133 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 148 through 149
      removed outlier: 4.658A  pdb=" N   TRP B 143 " --> pdb=" O   GLN B 149 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 3 through 6
      removed outlier: 3.646A  pdb=" N   GLU C   5 " --> pdb=" O   LYS C  23 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 33 through 35
    Processing sheet with id=AA7, first strand: chain 'C' and resid 89 through 91
    Processing sheet with id=AA8, first strand: chain 'C' and resid 121 through 123
      removed outlier: 5.886A  pdb=" N   TRP C 170 " --> pdb=" O   GLY C 143 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 121 through 123
      removed outlier: 5.886A  pdb=" N   TRP C 170 " --> pdb=" O   GLY C 143 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   LEU C 169 " --> pdb=" O   ASN C 166 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 185 through 187

    384 hydrogen bonds defined for protein.
    1088 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.11

  Time building geometry restraints manager: 2.34 seconds

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

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

  Histogram of bond angle deviations from ideal:
        0.00 -     4.95: 9361
        4.95 -     9.89: 212
        9.89 -    14.84: 3
       14.84 -    19.79: 3
       19.79 -    24.74: 3
  Bond angle restraints: 9582
  Sorted by residual:
  angle pdb=" C03 ZGS A 601 "
        pdb=" C04 ZGS A 601 "
        pdb=" C05 ZGS A 601 "
      ideal   model   delta    sigma   weight residual
     127.34  152.08  -24.74 3.00e+00 1.11e-01 6.80e+01
  angle pdb=" C09 ZGS A 601 "
        pdb=" C10 ZGS A 601 "
        pdb=" C11 ZGS A 601 "
      ideal   model   delta    sigma   weight residual
     127.16  151.03  -23.87 3.00e+00 1.11e-01 6.33e+01
  angle pdb=" C06 ZGS A 601 "
        pdb=" C07 ZGS A 601 "
        pdb=" C08 ZGS A 601 "
      ideal   model   delta    sigma   weight residual
     127.52  151.32  -23.80 3.00e+00 1.11e-01 6.29e+01
  angle pdb=" C04 ZGS A 601 "
        pdb=" C05 ZGS A 601 "
        pdb=" C06 ZGS A 601 "
      ideal   model   delta    sigma   weight residual
     110.70  129.66  -18.96 3.00e+00 1.11e-01 3.99e+01
  angle pdb=" C02 ZGS A 601 "
        pdb=" C03 ZGS A 601 "
        pdb=" C04 ZGS A 601 "
      ideal   model   delta    sigma   weight residual
     127.67  111.44   16.23 3.00e+00 1.11e-01 2.93e+01
  ... (remaining 9577 not shown)

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

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 849
       0.050 -    0.100: 225
       0.100 -    0.150: 68
       0.150 -    0.200: 9
       0.200 -    0.250: 5
  Chirality restraints: 1156
  Sorted by residual:
  chirality pdb=" C1BALMT A 602 "
            pdb=" C2BALMT A 602 "
            pdb=" O1BALMT A 602 "
            pdb=" O5BALMT A 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.20   -2.45    0.25 2.00e-01 2.50e+01 1.56e+00
  chirality pdb=" C1B LMT A 607 "
            pdb=" C2B LMT A 607 "
            pdb=" O1B LMT A 607 "
            pdb=" O5B LMT A 607 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.20   -2.43    0.23 2.00e-01 2.50e+01 1.31e+00
  chirality pdb=" C1B LMT A 608 "
            pdb=" C2B LMT A 608 "
            pdb=" O1B LMT A 608 "
            pdb=" O5B LMT A 608 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.20   -2.42    0.22 2.00e-01 2.50e+01 1.18e+00
  ... (remaining 1153 not shown)

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

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

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=0.98
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             14.640
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     18.190
  Find NCS groups from input model:        0.080
  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:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.012   0.126   7037  Z= 0.765
  Angle     :  1.387  24.737   9582  Z= 0.547
  Chirality :  0.053   0.250   1156
  Planarity :  0.006   0.058   1130
  Dihedral  : 29.930 147.692   3050
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.54 %
    Favored  : 93.34 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  :  7.55 %
    Favored  : 91.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.42 (0.27), residues: 868
  helix:  0.47 (0.24), residues: 385
  sheet: -0.76 (0.43), residues: 150
  loop : -2.76 (0.30), residues: 333

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

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

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 132
  time to evaluate  : 0.612 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 ARG cc_start: 0.7242 (mmm-85) cc_final: 0.6932 (ttm-80)
REVERT: A  159 TYR cc_start: 0.8602 (t80) cc_final: 0.8345 (t80)
REVERT: A  173 ARG cc_start: 0.7234 (mtt180) cc_final: 0.6781 (mtt-85)
REVERT: A  199 VAL cc_start: 0.8805 (t) cc_final: 0.8386 (m)
REVERT: A  288 HIS cc_start: 0.7354 (t-90) cc_final: 0.6738 (t-90)
REVERT: A  296 MET cc_start: 0.6886 (mmt) cc_final: 0.6637 (mmp)
REVERT: A  413 GLN cc_start: 0.8528 (mm110) cc_final: 0.8012 (mt0)
  outliers start: 5
  outliers final: 0
  residues processed: 135
  average time/residue: 0.1922
  time to fit residues: 34.5196
Evaluate side-chains
  97 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.636 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 22 optimal weight:    5.9990
   chunk 43 optimal weight:    0.6980
   chunk 34 optimal weight:    0.5980
   chunk 67 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9990
   chunk 50 optimal weight:    0.2980
   chunk 78 optimal weight:    0.8980
   overall best weight:    0.6980

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

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

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.170506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.136674 restraints weight = 37608.871|
|-----------------------------------------------------------------------------|
r_work (start): 0.3588 rms_B_bonded: 6.42
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3589
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3589 r_free = 0.3589    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3589 r_free = 0.3589    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3589
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.1771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.080   7037  Z= 0.301
  Angle     :  0.895   9.929   9582  Z= 0.382
  Chirality :  0.052   0.304   1156
  Planarity :  0.005   0.057   1130
  Dihedral  : 19.406 156.238   1869
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.43 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 14.60 %
    Favored  : 83.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.82 (0.28), residues: 868
  helix:  1.38 (0.25), residues: 381
  sheet: -1.12 (0.41), residues: 175
  loop : -2.72 (0.31), residues: 312

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

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

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 102
  time to evaluate  : 0.697 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 ARG cc_start: 0.7873 (mmm-85) cc_final: 0.7536 (ttm-80)
REVERT: A  164 MET cc_start: 0.8261 (mmt) cc_final: 0.8000 (mmm)
REVERT: A  172 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7943 (mt-10)
REVERT: B  110 GLN cc_start: 0.7180 (tt0) cc_final: 0.6920 (mt0)
REVERT: B  196 PHE cc_start: 0.8032 (m-80) cc_final: 0.7752 (m-80)
  outliers start: 13
  outliers final: 8
  residues processed: 110
  average time/residue: 0.1872
  time to fit residues: 27.7746
Evaluate side-chains
  106 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 98
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 ASN
Chi-restraints excluded: chain A residue  359 ILE
Chi-restraints excluded: chain A residue  439 SER
Chi-restraints excluded: chain B residue    4 ILE
Chi-restraints excluded: chain B residue    5 ASN
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain C residue  151 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 54 optimal weight:    0.6980
   chunk 23 optimal weight:    6.9990
   chunk 77 optimal weight:    0.6980
   chunk 50 optimal weight:    0.4980
   chunk 0 optimal weight:    4.9990
   chunk 73 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 3 optimal weight:    0.5980
   chunk 33 optimal weight:    0.5980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3971 r_free = 0.3971 target = 0.170222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.136247 restraints weight = 38144.635|
|-----------------------------------------------------------------------------|
r_work (start): 0.3586 rms_B_bonded: 6.51
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3585
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3585 r_free = 0.3585    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3585 r_free = 0.3585    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3585
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.2017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   7037  Z= 0.255
  Angle     :  0.736   9.712   9582  Z= 0.333
  Chirality :  0.045   0.320   1156
  Planarity :  0.005   0.055   1130
  Dihedral  : 14.429 150.906   1869
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.31 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 15.44 %
    Favored  : 82.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.60 (0.29), residues: 868
  helix:  1.68 (0.26), residues: 379
  sheet: -1.15 (0.41), residues: 175
  loop : -2.64 (0.31), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  95 
 HIS   0.002   0.001   HIS A 156 
 PHE   0.021   0.002   PHE B  89 
 TYR   0.011   0.001   TYR A 291 
 ARG   0.005   0.001   ARG B 104 

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

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 102
  time to evaluate  : 0.643 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 ARG cc_start: 0.7843 (mmm-85) cc_final: 0.7459 (ttm-80)
REVERT: A  173 ARG cc_start: 0.7268 (mtt180) cc_final: 0.7059 (mtt-85)
REVERT: A  288 HIS cc_start: 0.6443 (t-170) cc_final: 0.5255 (t-170)
REVERT: A  291 TYR cc_start: 0.6698 (OUTLIER) cc_final: 0.6276 (t80)
REVERT: A  296 MET cc_start: 0.7458 (OUTLIER) cc_final: 0.6597 (tpp)
REVERT: A  319 ASN cc_start: 0.8109 (OUTLIER) cc_final: 0.7789 (m-40)
REVERT: B  110 GLN cc_start: 0.7118 (tt0) cc_final: 0.6896 (mt0)
REVERT: B  196 PHE cc_start: 0.8017 (m-80) cc_final: 0.7725 (m-80)
  outliers start: 13
  outliers final: 4
  residues processed: 109
  average time/residue: 0.1868
  time to fit residues: 27.5101
Evaluate side-chains
  105 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 98
  time to evaluate  : 0.701 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  296 MET
Chi-restraints excluded: chain A residue  319 ASN
Chi-restraints excluded: chain A residue  480 ILE
Chi-restraints excluded: chain B residue    5 ASN
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  112 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 71 optimal weight:    0.9990
   chunk 36 optimal weight:    7.9990
   chunk 15 optimal weight:    0.6980
   chunk 65 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9990
   chunk 69 optimal weight:    0.5980
   chunk 79 optimal weight:    6.9990
   chunk 7 optimal weight:    0.9990
   chunk 68 optimal weight:    0.6980
   chunk 53 optimal weight:    3.9990
   chunk 70 optimal weight:    0.0870
   overall best weight:    0.6160

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.169670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.135029 restraints weight = 34368.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.3566 rms_B_bonded: 6.15
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3566
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3566 r_free = 0.3566    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3566 r_free = 0.3566    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3566
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.2230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   7037  Z= 0.249
  Angle     :  0.690  10.344   9582  Z= 0.318
  Chirality :  0.042   0.297   1156
  Planarity :  0.005   0.055   1130
  Dihedral  : 12.745 148.770   1869
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.19 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 15.94 %
    Favored  : 82.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.48 (0.29), residues: 868
  helix:  1.78 (0.26), residues: 380
  sheet: -1.12 (0.42), residues: 173
  loop : -2.56 (0.32), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C  95 
 HIS   0.004   0.002   HIS A 288 
 PHE   0.027   0.002   PHE A 367 
 TYR   0.012   0.001   TYR A 358 
 ARG   0.004   0.001   ARG B 104 

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

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 0.701 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 ARG cc_start: 0.7776 (mmm-85) cc_final: 0.7353 (ttm-80)
REVERT: A  291 TYR cc_start: 0.6849 (OUTLIER) cc_final: 0.6421 (t80)
REVERT: A  296 MET cc_start: 0.7409 (OUTLIER) cc_final: 0.6478 (tpp)
REVERT: B  196 PHE cc_start: 0.8007 (m-80) cc_final: 0.7740 (m-80)
  outliers start: 12
  outliers final: 6
  residues processed: 105
  average time/residue: 0.1966
  time to fit residues: 27.6276
Evaluate side-chains
  103 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.669 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  296 MET
Chi-restraints excluded: chain A residue  439 SER
Chi-restraints excluded: chain A residue  480 ILE
Chi-restraints excluded: chain A residue  484 LEU
Chi-restraints excluded: chain B residue    5 ASN
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  112 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 49 optimal weight:    0.7980
   chunk 67 optimal weight:    0.7980
   chunk 50 optimal weight:    0.0980
   chunk 27 optimal weight:    0.4980
   chunk 29 optimal weight:    0.6980
   chunk 10 optimal weight:    0.7980
   chunk 65 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 22 optimal weight:   10.0000
   overall best weight:    0.5780

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.169442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.139077 restraints weight = 39493.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.3621 rms_B_bonded: 5.51
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3619
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3619 r_free = 0.3619    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3619 r_free = 0.3619    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3619
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.2417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   7037  Z= 0.238
  Angle     :  0.680  10.449   9582  Z= 0.314
  Chirality :  0.042   0.294   1156
  Planarity :  0.005   0.052   1130
  Dihedral  : 12.152 149.481   1869
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.61 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 16.28 %
    Favored  : 82.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.29), residues: 868
  helix:  1.91 (0.26), residues: 379
  sheet: -1.11 (0.42), residues: 173
  loop : -2.54 (0.32), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 103 
 HIS   0.002   0.001   HIS A 288 
 PHE   0.020   0.001   PHE B  89 
 TYR   0.010   0.001   TYR B  48 
 ARG   0.004   0.001   ARG B 104 

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

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.709 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 ARG cc_start: 0.7882 (mmm-85) cc_final: 0.7451 (ttm-80)
REVERT: A  291 TYR cc_start: 0.6850 (OUTLIER) cc_final: 0.6387 (t80)
REVERT: A  296 MET cc_start: 0.7273 (OUTLIER) cc_final: 0.6317 (tpp)
REVERT: B  196 PHE cc_start: 0.7941 (m-80) cc_final: 0.7691 (m-80)
  outliers start: 9
  outliers final: 6
  residues processed: 100
  average time/residue: 0.2077
  time to fit residues: 27.5212
Evaluate side-chains
  102 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  296 MET
Chi-restraints excluded: chain A residue  439 SER
Chi-restraints excluded: chain A residue  480 ILE
Chi-restraints excluded: chain A residue  484 LEU
Chi-restraints excluded: chain B residue    5 ASN
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  141 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 24 optimal weight:    0.6980
   chunk 57 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   chunk 72 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0050
   chunk 44 optimal weight:    4.9990
   chunk 70 optimal weight:    0.2980
   chunk 13 optimal weight:    0.6980
   chunk 41 optimal weight:    0.5980
   overall best weight:    0.4594

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.170893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.143142 restraints weight = 36273.355|
|-----------------------------------------------------------------------------|
r_work (start): 0.3605 rms_B_bonded: 5.35
r_work (final): 0.3605
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3597
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3597 r_free = 0.3597    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3597 r_free = 0.3597    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3597
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.2532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   7037  Z= 0.210
  Angle     :  0.666  10.440   9582  Z= 0.307
  Chirality :  0.041   0.288   1156
  Planarity :  0.005   0.053   1130
  Dihedral  : 11.786 150.458   1869
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.72 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 15.94 %
    Favored  : 82.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.30 (0.29), residues: 868
  helix:  1.90 (0.26), residues: 386
  sheet: -1.17 (0.41), residues: 176
  loop : -2.42 (0.32), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.002   TRP A 103 
 HIS   0.003   0.002   HIS A 288 
 PHE   0.026   0.001   PHE A 367 
 TYR   0.010   0.001   TYR A 251 
 ARG   0.004   0.000   ARG A 173 

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

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.648 
Fit side-chains
REVERT: A  100 ARG cc_start: 0.7932 (mmm-85) cc_final: 0.7545 (ttm-80)
REVERT: A  296 MET cc_start: 0.7203 (OUTLIER) cc_final: 0.6323 (tpp)
REVERT: A  354 LYS cc_start: 0.7408 (ttpt) cc_final: 0.7200 (ttpp)
  outliers start: 10
  outliers final: 8
  residues processed: 102
  average time/residue: 0.1974
  time to fit residues: 26.8444
Evaluate side-chains
  104 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 GLU
Chi-restraints excluded: chain A residue  296 MET
Chi-restraints excluded: chain A residue  439 SER
Chi-restraints excluded: chain A residue  480 ILE
Chi-restraints excluded: chain A residue  484 LEU
Chi-restraints excluded: chain B residue    4 ILE
Chi-restraints excluded: chain B residue    5 ASN
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  141 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 27 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 60 optimal weight:    0.3980
   chunk 55 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 52 optimal weight:    0.6980
   chunk 6 optimal weight:    0.0030
   chunk 70 optimal weight:    0.0870
   chunk 45 optimal weight:    7.9990
   overall best weight:    0.3968

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.170781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.142206 restraints weight = 41789.696|
|-----------------------------------------------------------------------------|
r_work (start): 0.3668 rms_B_bonded: 5.31
r_work (final): 0.3668
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3669
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3669 r_free = 0.3669    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3669 r_free = 0.3669    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3669
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.2662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7037  Z= 0.194
  Angle     :  0.655  10.701   9582  Z= 0.304
  Chirality :  0.041   0.283   1156
  Planarity :  0.005   0.054   1130
  Dihedral  : 11.410 152.188   1869
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.26 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 17.45 %
    Favored  : 80.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.29), residues: 868
  helix:  1.94 (0.26), residues: 386
  sheet: -1.18 (0.41), residues: 171
  loop : -2.36 (0.32), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.002   TRP A 103 
 HIS   0.004   0.002   HIS A 288 
 PHE   0.016   0.001   PHE B  89 
 TYR   0.009   0.001   TYR B  48 
 ARG   0.002   0.000   ARG A  34 

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

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 100
  time to evaluate  : 0.685 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 ARG cc_start: 0.7794 (mmm-85) cc_final: 0.7357 (ttm-80)
REVERT: A  291 TYR cc_start: 0.6642 (OUTLIER) cc_final: 0.6276 (t80)
REVERT: A  296 MET cc_start: 0.7168 (OUTLIER) cc_final: 0.6192 (tpp)
REVERT: A  354 LYS cc_start: 0.7516 (ttpt) cc_final: 0.7278 (ttpp)
  outliers start: 10
  outliers final: 6
  residues processed: 104
  average time/residue: 0.2016
  time to fit residues: 27.7872
Evaluate side-chains
  105 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 97
  time to evaluate  : 0.774 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 GLU
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  296 MET
Chi-restraints excluded: chain A residue  439 SER
Chi-restraints excluded: chain B residue    4 ILE
Chi-restraints excluded: chain B residue    5 ASN
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  141 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 75 optimal weight:    0.7980
   chunk 81 optimal weight:    0.5980
   chunk 14 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 68 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 47 optimal weight:    0.5980
   chunk 8 optimal weight:    0.5980
   chunk 4 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9990
   chunk 67 optimal weight:    0.0370
   overall best weight:    0.4858

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.170120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.137299 restraints weight = 35510.914|
|-----------------------------------------------------------------------------|
r_work (start): 0.3611 rms_B_bonded: 6.03
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3610
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3610 r_free = 0.3610    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3609 r_free = 0.3609    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3609
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.2739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   7037  Z= 0.215
  Angle     :  0.661  10.527   9582  Z= 0.308
  Chirality :  0.041   0.284   1156
  Planarity :  0.005   0.055   1130
  Dihedral  : 11.204 153.057   1869
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.49 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 17.79 %
    Favored  : 80.54 %
  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: -0.23 (0.29), residues: 868
  helix:  1.96 (0.26), residues: 385
  sheet: -1.12 (0.41), residues: 171
  loop : -2.37 (0.33), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.058   0.002   TRP A 103 
 HIS   0.005   0.002   HIS A 288 
 PHE   0.021   0.001   PHE A 367 
 TYR   0.010   0.001   TYR A 358 
 ARG   0.006   0.001   ARG A 173 

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

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.629 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 ARG cc_start: 0.7860 (mmm-85) cc_final: 0.7374 (ttm-80)
REVERT: A  173 ARG cc_start: 0.6918 (mtt-85) cc_final: 0.6599 (mtt-85)
REVERT: A  291 TYR cc_start: 0.6697 (OUTLIER) cc_final: 0.6304 (t80)
REVERT: A  296 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.6375 (tpp)
REVERT: A  354 LYS cc_start: 0.7576 (ttpt) cc_final: 0.7320 (ttpp)
  outliers start: 10
  outliers final: 6
  residues processed: 103
  average time/residue: 0.1919
  time to fit residues: 26.4131
Evaluate side-chains
  107 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 99
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 GLU
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  296 MET
Chi-restraints excluded: chain A residue  439 SER
Chi-restraints excluded: chain B residue    4 ILE
Chi-restraints excluded: chain B residue    5 ASN
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  141 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 69 optimal weight:    0.5980
   chunk 51 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   chunk 78 optimal weight:    4.9990
   chunk 82 optimal weight:    1.9990
   chunk 48 optimal weight:    0.2980
   chunk 32 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 81 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.8982

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.166657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.135907 restraints weight = 32774.680|
|-----------------------------------------------------------------------------|
r_work (start): 0.3589 rms_B_bonded: 5.01
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3586
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3586 r_free = 0.3586    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3586 r_free = 0.3586    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3586
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
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      :  0.005   0.068   7037  Z= 0.318
  Angle     :  0.718  10.220   9582  Z= 0.337
  Chirality :  0.043   0.298   1156
  Planarity :  0.005   0.057   1130
  Dihedral  : 11.426 153.849   1869
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.66 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 17.79 %
    Favored  : 80.54 %
  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: -0.48 (0.29), residues: 868
  helix:  1.76 (0.26), residues: 383
  sheet: -1.25 (0.41), residues: 170
  loop : -2.48 (0.33), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP C  95 
 HIS   0.007   0.003   HIS A 288 
 PHE   0.027   0.002   PHE B  89 
 TYR   0.012   0.002   TYR A 251 
 ARG   0.009   0.001   ARG A 173 

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

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.537 
Fit side-chains
REVERT: A  100 ARG cc_start: 0.7939 (mmm-85) cc_final: 0.7513 (ttm-80)
REVERT: A  291 TYR cc_start: 0.6927 (OUTLIER) cc_final: 0.6484 (t80)
REVERT: A  296 MET cc_start: 0.7337 (OUTLIER) cc_final: 0.6350 (tpp)
REVERT: A  354 LYS cc_start: 0.7634 (ttpt) cc_final: 0.7354 (ttpp)
  outliers start: 10
  outliers final: 6
  residues processed: 101
  average time/residue: 0.1954
  time to fit residues: 26.5529
Evaluate side-chains
  102 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 0.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 GLU
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  296 MET
Chi-restraints excluded: chain A residue  439 SER
Chi-restraints excluded: chain A residue  480 ILE
Chi-restraints excluded: chain B residue    5 ASN
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  141 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 80 optimal weight:    0.5980
   chunk 45 optimal weight:   40.0000
   chunk 31 optimal weight:    1.9990
   chunk 64 optimal weight:    4.9990
   chunk 59 optimal weight:    0.4980
   chunk 84 optimal weight:    4.9990
   chunk 70 optimal weight:    0.0470
   chunk 12 optimal weight:    0.9980
   chunk 77 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.5878

-------------------------------------------------------------------------------
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 319 ASN
A 414 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.168530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.136089 restraints weight = 28137.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.3591 rms_B_bonded: 5.16
r_work (final): 0.3591
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3585
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3585 r_free = 0.3585    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3586 r_free = 0.3586    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3586
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.2919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   7037  Z= 0.240
  Angle     :  0.673  10.575   9582  Z= 0.314
  Chirality :  0.042   0.292   1156
  Planarity :  0.005   0.057   1130
  Dihedral  : 11.188 153.712   1869
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.96 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 18.29 %
    Favored  : 80.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.44 (0.29), residues: 868
  helix:  1.80 (0.26), residues: 383
  sheet: -1.24 (0.42), residues: 165
  loop : -2.45 (0.32), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP A 103 
 HIS   0.002   0.001   HIS A 156 
 PHE   0.023   0.002   PHE A 367 
 TYR   0.011   0.001   TYR A 358 
 ARG   0.005   0.000   ARG A 173 

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

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.665 
Fit side-chains
REVERT: A  100 ARG cc_start: 0.7916 (mmm-85) cc_final: 0.7494 (ttm-80)
REVERT: A  291 TYR cc_start: 0.6792 (OUTLIER) cc_final: 0.6447 (t80)
REVERT: A  296 MET cc_start: 0.7298 (OUTLIER) cc_final: 0.6327 (tpp)
REVERT: A  354 LYS cc_start: 0.7565 (ttpt) cc_final: 0.7285 (ttpp)
  outliers start: 9
  outliers final: 6
  residues processed: 99
  average time/residue: 0.1989
  time to fit residues: 26.4044
Evaluate side-chains
  101 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 0.665 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 GLU
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  296 MET
Chi-restraints excluded: chain A residue  439 SER
Chi-restraints excluded: chain B residue    5 ASN
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  141 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 4 optimal weight:    0.3980
   chunk 66 optimal weight:    0.0870
   chunk 31 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9980
   chunk 85 optimal weight:    0.0770
   chunk 59 optimal weight:    0.8980
   chunk 63 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9990
   chunk 73 optimal weight:    0.0040
   chunk 57 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.2528

-------------------------------------------------------------------------------
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 319 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.171549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.138554 restraints weight = 35490.627|
|-----------------------------------------------------------------------------|
r_work (start): 0.3626 rms_B_bonded: 6.10
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3624
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3624 r_free = 0.3624    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3624 r_free = 0.3624    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3624
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.3021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7037  Z= 0.171
  Angle     :  0.667  10.940   9582  Z= 0.310
  Chirality :  0.040   0.280   1156
  Planarity :  0.005   0.057   1130
  Dihedral  : 10.767 155.209   1869
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.02 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 18.96 %
    Favored  : 79.70 %
  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: -0.31 (0.29), residues: 868
  helix:  1.87 (0.26), residues: 387
  sheet: -1.16 (0.41), residues: 177
  loop : -2.42 (0.34), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP A 103 
 HIS   0.003   0.001   HIS A 288 
 PHE   0.014   0.001   PHE B  89 
 TYR   0.009   0.001   TYR A 251 
 ARG   0.010   0.001   ARG A 173 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2873.62 seconds
wall clock time: 52 minutes 24.35 seconds (3144.35 seconds total)