Starting phenix.real_space_refine
on Fri Jul  3 07:51:13 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8c1b_16377/07_2026/8c1b_16377.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8c1b_16377/07_2026/8c1b_16377.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/8c1b_16377/07_2026/8c1b_16377.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8c1b_16377/07_2026/8c1b_16377.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8c1b_16377/07_2026/8c1b_16377.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8c1b_16377/07_2026/8c1b_16377.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8c1b_16377/07_2026/8c1b_16377.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8c1b_16377/07_2026/8c1b_16377.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.001 sd=   0.057
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
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
     S      27      5.16       5
     C    4105      2.51       5
     N    1119      2.21       5
     O    1318      1.98       5
     H    6106      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 12675
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "H"
      Number of atoms: 4913
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 319, 4913
          Classifications: {'peptide': 319}
          Modifications used: {'COO': 1, 'NH1NOTPRO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 296}
    Chain: "R"
      Number of atoms: 2646
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 169, 2646
          Classifications: {'peptide': 169}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 162}
    Chain: "X"
      Number of atoms: 4913
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 319, 4913
          Classifications: {'peptide': 319}
          Modifications used: {'COO': 1, 'NH1NOTPRO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 296}
    Chain: "A"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen chiralities: 5
    Chain: "B"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen chiralities: 3
    Chain: "C"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen chiralities: 5
    Chain: "R"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen chiralities: 3
  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N   GLY H 315 " occ=0.00
      ... (5 atoms not shown)
      pdb=" HA3 GLY H 315 " occ=0.00
    residue:
      pdb=" N   HIS H 316 " occ=0.00
      ... (15 atoms not shown)
      pdb=" HE2 HIS H 316 " occ=0.00
    residue:
      pdb=" N   GLY X 315 " occ=0.00
      ... (5 atoms not shown)
      pdb=" HA3 GLY X 315 " occ=0.00
    residue:
      pdb=" N   HIS X 316 " occ=0.00
      ... (15 atoms not shown)
      pdb=" HE2 HIS X 316 " occ=0.00
  Time building chain proxies: 2.14, per 1000 atoms: 0.17
  Number of scatterers: 12675
  At special positions: 0
  Unit cell: (96.3713, 122.278, 103.625, 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      27     16.00
     O    1318      8.00
     N    1119      7.00
     C    4105      6.00
     H    6106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, symmetry=0
    Simple disulfide: pdb=" SG  CYS H 237 " - pdb=" SG  CYS X 325 " distance=2.06
    Simple disulfide: pdb=" SG  CYS H 251 " - pdb=" SG  CYS H 309 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H 325 " - pdb=" SG  CYS X 237 " distance=2.05
    Simple disulfide: pdb=" SG  CYS H 355 " - pdb=" SG  CYS H 415 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H 461 " - pdb=" SG  CYS H 521 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R  26 " - pdb=" SG  CYS R  68 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R 107 " - pdb=" SG  CYS R 151 " distance=2.04
    Simple disulfide: pdb=" SG  CYS X 251 " - pdb=" SG  CYS X 309 " distance=2.04
    Simple disulfide: pdb=" SG  CYS X 355 " - pdb=" SG  CYS X 415 " distance=2.03
    Simple disulfide: pdb=" SG  CYS X 461 " - pdb=" SG  CYS X 521 " 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
      
  Atom "HETATM12645  O5  NAG R 501 .*.     O  " rejected from bonding due to valence issues.
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    ALPHA1-3
      " BMA A   3 " - " MAN A   4 "
      " BMA C   3 " - " MAN C   4 "
    ALPHA1-4
      " NAG B   2 " - " MAN B   3 "
    ALPHA1-6
      " BMA A   3 " - " MAN A   5 "
      " BMA C   3 " - " MAN C   5 "
    BETA1-4
      " NAG A   1 " - " NAG A   2 "
      " NAG A   2 " - " BMA A   3 "
      " NAG B   1 " - " NAG B   2 "
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
    NAG-ASN
      " NAG A   1 " - " ASN H 391 "
      " NAG B   1 " - " ASN R  42 "
      " NAG C   1 " - " ASN X 391 "
      " NAG R 501 " - " ASN R 166 "
      " NAG R 502 " - " ASN R  21 "
      " NAG R 503 " - " ASN R 135 "
  Time building additional restraints: 1.08
  Conformation dependent library (CDL) restraints added in 388.8 milliseconds
  

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1524

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 19 sheets defined
      9.9% alpha, 48.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'H' and resid 273 through 275
      No H-bonds generated for 'chain 'H' and resid 273 through 275'
    Processing helix  chain 'H' and resid 298 through 303
    Processing helix  chain 'H' and resid 341 through 347
    Processing helix  chain 'H' and resid 403 through 409
    Processing helix  chain 'H' and resid 483 through 485
      No H-bonds generated for 'chain 'H' and resid 483 through 485'
    Processing helix  chain 'H' and resid 509 through 516
    Processing helix  chain 'R' and resid 59 through 63
    Processing helix  chain 'R' and resid 111 through 113
      No H-bonds generated for 'chain 'R' and resid 111 through 113'
    Processing helix  chain 'R' and resid 142 through 146
      removed outlier: 3.698A  pdb=" N   SER R 146 " --> pdb=" O   VAL R 143 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 273 through 275
      No H-bonds generated for 'chain 'X' and resid 273 through 275'
    Processing helix  chain 'X' and resid 298 through 303
    Processing helix  chain 'X' and resid 341 through 347
    Processing helix  chain 'X' and resid 403 through 409
    Processing helix  chain 'X' and resid 483 through 485
      No H-bonds generated for 'chain 'X' and resid 483 through 485'
    Processing helix  chain 'X' and resid 510 through 516
    Processing sheet with id=AA1, first strand: chain 'H' and resid 277 through 284
      removed outlier: 6.381A  pdb=" N   ALA H 288 " --> pdb=" O   GLY H 255 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   GLY H 255 " --> pdb=" O   ALA H 288 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   GLN H 248 " --> pdb=" O   SER H 235 " (cutoff:3.500A)
      removed outlier: 5.854A  pdb=" N   ALA X 288 " --> pdb=" O   GLY X 255 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 270 through 271
    Processing sheet with id=AA3, first strand: chain 'H' and resid 334 through 337
      removed outlier: 4.712A  pdb=" N   ASP H 359 " --> pdb=" O   LEU H 394 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   LEU H 394 " --> pdb=" O   ASP H 359 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 368 through 373
    Processing sheet with id=AA5, first strand: chain 'H' and resid 441 through 446
      removed outlier: 5.532A  pdb=" N   PHE H 500 " --> pdb=" O   ASN H 465 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 441 through 446
      removed outlier: 5.532A  pdb=" N   PHE H 500 " --> pdb=" O   ASN H 465 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 480 through 481
    Processing sheet with id=AA8, first strand: chain 'R' and resid 6 through 10
    Processing sheet with id=AA9, first strand: chain 'R' and resid 15 through 17
      removed outlier: 6.568A  pdb=" N   ILE R  16 " --> pdb=" O   PHE R  84 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'R' and resid 44 through 46
      removed outlier: 4.480A  pdb=" N   TRP R  39 " --> pdb=" O   SER R  46 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'R' and resid 88 through 92
    Processing sheet with id=AB3, first strand: chain 'R' and resid 96 through 98
      removed outlier: 6.709A  pdb=" N   VAL R  97 " --> pdb=" O   ILE R 170 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   THR R 148 " --> pdb=" O   LYS R 122 " (cutoff:3.500A)
      removed outlier: 4.826A  pdb=" N   LYS R 122 " --> pdb=" O   THR R 148 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   TYR R 150 " --> pdb=" O   TYR R 120 " (cutoff:3.500A)
      removed outlier: 4.935A  pdb=" N   TYR R 120 " --> pdb=" O   TYR R 150 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   THR R 152 " --> pdb=" O   VAL R 118 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   VAL R 118 " --> pdb=" O   THR R 152 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   LYS R 128 " --> pdb=" O   TYR R 120 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   LYS R 122 " --> pdb=" O   ALA R 126 " (cutoff:3.500A)
      removed outlier: 5.679A  pdb=" N   ALA R 126 " --> pdb=" O   LYS R 122 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'R' and resid 96 through 98
      removed outlier: 6.709A  pdb=" N   VAL R  97 " --> pdb=" O   ILE R 170 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'X' and resid 270 through 271
    Processing sheet with id=AB6, first strand: chain 'X' and resid 334 through 337
      removed outlier: 3.774A  pdb=" N   ASP X 359 " --> pdb=" O   LEU X 394 " (cutoff:3.500A)
      removed outlier: 6.128A  pdb=" N   LEU X 394 " --> pdb=" O   ASP X 359 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'X' and resid 368 through 373
    Processing sheet with id=AB8, first strand: chain 'X' and resid 441 through 446
      removed outlier: 5.418A  pdb=" N   PHE X 500 " --> pdb=" O   ASN X 465 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'X' and resid 441 through 446
      removed outlier: 5.418A  pdb=" N   PHE X 500 " --> pdb=" O   ASN X 465 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'X' and resid 480 through 481

    292 hydrogen bonds defined for protein.
    747 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: 2.17

  Time building geometry restraints manager: 1.50 seconds

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

  Histogram of bond lengths:
        0.83 -     1.04: 6106
        1.04 -     1.24: 798
        1.24 -     1.44: 2168
        1.44 -     1.64: 3731
        1.64 -     1.84: 34
  Bond restraints: 12837
  Sorted by residual:
  bond pdb=" N   ASP X 224 "
       pdb=" H1  ASP X 224 "
    ideal  model  delta    sigma   weight residual
    0.960  0.860  0.100 2.00e-02 2.50e+03 2.50e+01
  bond pdb=" N   ASP H 224 "
       pdb=" H1  ASP H 224 "
    ideal  model  delta    sigma   weight residual
    0.960  0.860  0.100 2.00e-02 2.50e+03 2.49e+01
  bond pdb=" C1  NAG R 501 "
       pdb=" O5  NAG R 501 "
    ideal  model  delta    sigma   weight residual
    1.406  1.483 -0.077 2.00e-02 2.50e+03 1.49e+01
  bond pdb=" CA  VAL R  22 "
       pdb=" CB  VAL R  22 "
    ideal  model  delta    sigma   weight residual
    1.540  1.590 -0.050 1.36e-02 5.41e+03 1.35e+01
  bond pdb=" C1  NAG R 502 "
       pdb=" O5  NAG R 502 "
    ideal  model  delta    sigma   weight residual
    1.406  1.456 -0.050 2.00e-02 2.50e+03 6.25e+00
  ... (remaining 12832 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.49: 22002
        2.49 -     4.97: 891
        4.97 -     7.46: 139
        7.46 -     9.95: 15
        9.95 -    12.43: 4
  Bond angle restraints: 23051
  Sorted by residual:
  angle pdb=" C   ASN R 166 "
        pdb=" CA  ASN R 166 "
        pdb=" CB  ASN R 166 "
      ideal   model   delta    sigma   weight residual
     109.84  121.81  -11.97 1.63e+00 3.76e-01 5.39e+01
  angle pdb=" CA  GLN R 157 "
        pdb=" CB  GLN R 157 "
        pdb=" CG  GLN R 157 "
      ideal   model   delta    sigma   weight residual
     114.10  126.53  -12.43 2.00e+00 2.50e-01 3.87e+01
  angle pdb=" N   VAL R  22 "
        pdb=" CA  VAL R  22 "
        pdb=" CB  VAL R  22 "
      ideal   model   delta    sigma   weight residual
     111.23  119.92   -8.69 1.65e+00 3.67e-01 2.77e+01
  angle pdb=" C   GLU H 319 "
        pdb=" CA  GLU H 319 "
        pdb=" CB  GLU H 319 "
      ideal   model   delta    sigma   weight residual
     110.62  101.26    9.36 1.86e+00 2.89e-01 2.53e+01
  angle pdb=" C   GLY R  64 "
        pdb=" N   GLU R  65 "
        pdb=" CA  GLU R  65 "
      ideal   model   delta    sigma   weight residual
     120.82  127.56   -6.74 1.41e+00 5.03e-01 2.29e+01
  ... (remaining 23046 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.80: 5384
       17.80 -    35.61: 495
       35.61 -    53.41: 130
       53.41 -    71.22: 32
       71.22 -    89.02: 13
  Dihedral angle restraints: 6054
    sinusoidal: 3279
      harmonic: 2775
  Sorted by residual:
  dihedral pdb=" CB  CYS H 325 "
           pdb=" SG  CYS H 325 "
           pdb=" SG  CYS X 237 "
           pdb=" CB  CYS X 237 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -167.92   81.92     1      1.00e+01 1.00e-02 8.25e+01
  dihedral pdb=" CB  CYS H 237 "
           pdb=" SG  CYS H 237 "
           pdb=" SG  CYS X 325 "
           pdb=" CB  CYS X 325 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  166.28  -73.28     1      1.00e+01 1.00e-02 6.84e+01
  dihedral pdb=" C   ASN R 166 "
           pdb=" N   ASN R 166 "
           pdb=" CA  ASN R 166 "
           pdb=" CB  ASN R 166 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -139.35   16.75     0      2.50e+00 1.60e-01 4.49e+01
  ... (remaining 6051 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.115: 980
       0.115 -    0.229: 85
       0.229 -    0.344: 6
       0.344 -    0.458: 1
       0.458 -    0.572: 1
  Chirality restraints: 1073
  Sorted by residual:
  chirality pdb=" CA  ASN R 166 "
            pdb=" N   ASN R 166 "
            pdb=" C   ASN R 166 "
            pdb=" CB  ASN R 166 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.94    0.57 2.00e-01 2.50e+01 8.19e+00
  chirality pdb=" CG  LEU R  90 "
            pdb=" CB  LEU R  90 "
            pdb=" CD1 LEU R  90 "
            pdb=" CD2 LEU R  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.24   -0.34 2.00e-01 2.50e+01 2.97e+00
  chirality pdb=" CA  GLN R 157 "
            pdb=" N   GLN R 157 "
            pdb=" C   GLN R 157 "
            pdb=" CB  GLN R 157 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.56e+00
  ... (remaining 1070 not shown)

  Planarity restraints: 1911
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN R 166 "   -0.005 2.00e-02 2.50e+03   9.57e-02 1.15e+02
        pdb=" CG  ASN R 166 "   -0.119 2.00e-02 2.50e+03
        pdb=" OD1 ASN R 166 "    0.117 2.00e-02 2.50e+03
        pdb=" ND2 ASN R 166 "   -0.091 2.00e-02 2.50e+03
        pdb=" C1  NAG R 501 "    0.098 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN R 166 "    0.029 2.00e-02 2.50e+03   5.82e-02 3.39e+01
        pdb=" CG  ASN R 166 "   -0.101 2.00e-02 2.50e+03
        pdb=" OD1 ASN R 166 "    0.039 2.00e-02 2.50e+03
        pdb=" ND2 ASN R 166 "    0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR X 257 "    0.084 5.00e-02 4.00e+02   1.24e-01 2.46e+01
        pdb=" N   PRO X 258 "   -0.214 5.00e-02 4.00e+02
        pdb=" CA  PRO X 258 "    0.064 5.00e-02 4.00e+02
        pdb=" CD  PRO X 258 "    0.067 5.00e-02 4.00e+02
  ... (remaining 1908 not shown)

  Histogram of nonbonded interaction distances:
        1.71 -     2.29: 2448
        2.29 -     2.87: 26597
        2.87 -     3.45: 30408
        3.45 -     4.02: 43005
        4.02 -     4.60: 63202
  Nonbonded interactions: 165660
  Sorted by model distance:
  nonbonded pdb=" HE2 HIS H 477 "
            pdb=" O   LYS H 516 "
     model   vdw
     1.713 2.450
  nonbonded pdb="HE22 GLN H 234 "
            pdb=" O   SER X 235 "
     model   vdw
     1.733 2.450
  nonbonded pdb=" O   GLY R 124 "
            pdb="HH22 ARG X 390 "
     model   vdw
     1.737 2.450
  nonbonded pdb=" HE2 HIS X 477 "
            pdb=" O   LYS X 516 "
     model   vdw
     1.746 2.450
  nonbonded pdb=" HE  ARG X 522 "
            pdb=" OE1 GLN X 535 "
     model   vdw
     1.751 2.450
  ... (remaining 165655 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'H'
  selection = chain 'X'
}

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=0.00 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.780
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.090
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     12.090
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  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:0.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6966
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      :  0.007   0.077   6757  Z= 0.343
  Angle     :  1.411  34.775   9242  Z= 0.734
  Chirality :  0.068   0.572   1073
  Planarity :  0.009   0.124   1160
  Dihedral  : 14.825  89.022   2381
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  4.24 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  9.33 %
    Favored  : 90.39 %
  Cbeta Deviations :  0.26 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.06 (0.29), residues: 801
  helix: -1.61 (0.63), residues: 56
  sheet:  1.02 (0.27), residues: 357
  loop : -0.81 (0.29), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG R 106 
 TYR   0.021   0.003   TYR R  80 
 PHE   0.021   0.003   PHE X 318 
 TRP   0.035   0.004   TRP R  13 
 HIS   0.013   0.003   HIS H 381 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00738 /  0.34 ( 6731)
  covalent geometry    : angle       1.30665 /  0.71 ( 9174)
  SS BOND              : bond        0.01230 /  0.64 (   10)
  SS BOND              : angle       4.43173 /  2.67 (   20)
  hydrogen bonds       : bond        0.10524 /  7.46 (  260)
  hydrogen bonds       : angle       6.95266 /  4.92 (  747)
  link_ALPHA1-3        : bond        0.00490 /  0.25 (    2)
  link_ALPHA1-3        : angle       1.51056 /  0.95 (    6)
  link_ALPHA1-4        : bond        0.00467 /  0.25 (    1)
  link_ALPHA1-4        : angle       1.27286 /  0.91 (    3)
  link_ALPHA1-6        : bond        0.00406 /  0.20 (    2)
  link_ALPHA1-6        : angle       1.57731 /  1.05 (    6)
  link_BETA1-4         : bond        0.00377 /  0.20 (    5)
  link_BETA1-4         : angle       2.48239 /  1.25 (   15)
  link_NAG-ASN         : bond        0.01119 /  0.56 (    6)
  link_NAG-ASN         : angle      11.11506 /  6.55 (   18)

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

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

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 24
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 0
  residues processed: 25
  average time/residue: 0.1413
  time to fit residues: 5.4943
Evaluate side-chains
  20 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
X 389 GLN
X 419 HIS
X 474 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.080751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.068414 restraints weight = 108410.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 70)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.070420 restraints weight = 51006.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.071513 restraints weight = 31109.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.072326 restraints weight = 23079.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.072652 restraints weight = 19004.904|
|-----------------------------------------------------------------------------|
r_work (final): 0.4027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6910
moved from start:          0.1043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6757  Z= 0.144
  Angle     :  0.653   8.919   9242  Z= 0.328
  Chirality :  0.042   0.159   1073
  Planarity :  0.005   0.066   1160
  Dihedral  :  5.589  48.402    871
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  :  9.19 %
    Favored  : 89.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.66 (0.29), residues: 801
  helix: -1.58 (0.58), residues: 58
  sheet:  1.22 (0.26), residues: 376
  loop :  0.03 (0.33), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG X 486 
 TYR   0.005   0.001   TYR H 307 
 PHE   0.008   0.001   PHE H 445 
 TRP   0.014   0.001   TRP X 513 
 HIS   0.004   0.001   HIS R 134 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00307 /  0.14 ( 6731)
  covalent geometry    : angle       0.61290 /  0.32 ( 9174)
  SS BOND              : bond        0.00677 /  0.35 (   10)
  SS BOND              : angle       1.48145 /  0.89 (   20)
  hydrogen bonds       : bond        0.03711 /  2.57 (  260)
  hydrogen bonds       : angle       5.55671 /  3.97 (  747)
  link_ALPHA1-3        : bond        0.00515 /  0.26 (    2)
  link_ALPHA1-3        : angle       1.76029 /  1.11 (    6)
  link_ALPHA1-4        : bond        0.00588 /  0.31 (    1)
  link_ALPHA1-4        : angle       1.37245 /  0.90 (    3)
  link_ALPHA1-6        : bond        0.00234 /  0.12 (    2)
  link_ALPHA1-6        : angle       1.71412 /  1.08 (    6)
  link_BETA1-4         : bond        0.00231 /  0.14 (    5)
  link_BETA1-4         : angle       1.99677 /  1.15 (   15)
  link_NAG-ASN         : bond        0.00472 /  0.24 (    6)
  link_NAG-ASN         : angle       4.42848 /  2.63 (   18)

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

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

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 20
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 9
  outliers final: 3
  residues processed: 28
  average time/residue: 0.1064
  time to fit residues: 5.0916
Evaluate side-chains
  22 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 19
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  263 ILE
Chi-restraints excluded: chain R residue  166 ASN
Chi-restraints excluded: chain X residue  520 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 7 optimal weight:    8.9990
   chunk 42 optimal weight:    1.9990
   chunk 5 optimal weight:    9.9990
   chunk 35 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 65 optimal weight:    0.5980
   chunk 40 optimal weight:    2.9990
   overall best weight:    1.7188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H 381 HIS
H 389 GLN
** R  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
X 474 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.074042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.061058 restraints weight = 90427.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.062750 restraints weight = 38888.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.063544 restraints weight = 22912.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.063712 restraints weight = 17337.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.063986 restraints weight = 16429.286|
|-----------------------------------------------------------------------------|
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7198
moved from start:          0.2309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   6757  Z= 0.247
  Angle     :  0.703   8.182   9242  Z= 0.352
  Chirality :  0.041   0.150   1073
  Planarity :  0.005   0.051   1160
  Dihedral  :  5.487  48.935    871
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  9.05 %
    Favored  : 89.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.53 (0.29), residues: 801
  helix: -1.92 (0.57), residues: 58
  sheet:  1.25 (0.26), residues: 346
  loop : -0.05 (0.31), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG X 457 
 TYR   0.012   0.002   TYR R 149 
 PHE   0.013   0.002   PHE X 346 
 TRP   0.014   0.002   TRP H 407 
 HIS   0.008   0.002   HIS H 477 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00516 /  0.25 ( 6731)
  covalent geometry    : angle       0.65611 /  0.34 ( 9174)
  SS BOND              : bond        0.00351 /  0.21 (   10)
  SS BOND              : angle       2.59925 /  1.39 (   20)
  hydrogen bonds       : bond        0.03525 /  2.42 (  260)
  hydrogen bonds       : angle       5.22002 /  3.77 (  747)
  link_ALPHA1-3        : bond        0.00899 /  0.47 (    2)
  link_ALPHA1-3        : angle       1.47045 /  0.91 (    6)
  link_ALPHA1-4        : bond        0.00590 /  0.31 (    1)
  link_ALPHA1-4        : angle       2.00447 /  1.28 (    3)
  link_ALPHA1-6        : bond        0.00331 /  0.17 (    2)
  link_ALPHA1-6        : angle       1.51599 /  0.97 (    6)
  link_BETA1-4         : bond        0.00599 /  0.30 (    5)
  link_BETA1-4         : angle       2.37941 /  1.32 (   15)
  link_NAG-ASN         : bond        0.00850 /  0.45 (    6)
  link_NAG-ASN         : angle       4.43492 /  2.69 (   18)

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

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

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 21
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 8
  outliers final: 4
  residues processed: 28
  average time/residue: 0.1325
  time to fit residues: 5.7630
Evaluate side-chains
  23 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 19
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   68 CYS
Chi-restraints excluded: chain R residue  148 THR
Chi-restraints excluded: chain R residue  166 ASN
Chi-restraints excluded: chain X residue  520 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 56 optimal weight:    0.5980
   chunk 14 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 55 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 73 optimal weight:    2.9990
   overall best weight:    1.4586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** R  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.073852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.061359 restraints weight = 90238.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.062519 restraints weight = 39528.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.063457 restraints weight = 24999.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.063587 restraints weight = 18231.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.063885 restraints weight = 17715.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7222
moved from start:          0.2747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6757  Z= 0.191
  Angle     :  0.610   8.337   9242  Z= 0.304
  Chirality :  0.040   0.145   1073
  Planarity :  0.004   0.044   1160
  Dihedral  :  5.241  48.109    871
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 10.17 %
    Favored  : 88.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.67 (0.29), residues: 801
  helix: -1.87 (0.59), residues: 58
  sheet:  1.28 (0.26), residues: 347
  loop :  0.13 (0.32), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG X 457 
 TYR   0.006   0.001   TYR H 256 
 PHE   0.009   0.001   PHE H 445 
 TRP   0.013   0.002   TRP H 513 
 HIS   0.006   0.001   HIS H 477 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00403 /  0.19 ( 6731)
  covalent geometry    : angle       0.57104 /  0.29 ( 9174)
  SS BOND              : bond        0.00280 /  0.15 (   10)
  SS BOND              : angle       1.36511 /  0.75 (   20)
  hydrogen bonds       : bond        0.03152 /  2.17 (  260)
  hydrogen bonds       : angle       5.06589 /  3.66 (  747)
  link_ALPHA1-3        : bond        0.00542 /  0.28 (    2)
  link_ALPHA1-3        : angle       1.43256 /  0.86 (    6)
  link_ALPHA1-4        : bond        0.00125 /  0.07 (    1)
  link_ALPHA1-4        : angle       1.75745 /  1.15 (    3)
  link_ALPHA1-6        : bond        0.00306 /  0.15 (    2)
  link_ALPHA1-6        : angle       1.45998 /  0.99 (    6)
  link_BETA1-4         : bond        0.00384 /  0.21 (    5)
  link_BETA1-4         : angle       1.96097 /  1.14 (   15)
  link_NAG-ASN         : bond        0.00663 /  0.33 (    6)
  link_NAG-ASN         : angle       4.17948 /  2.51 (   18)

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

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

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 19
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 10
  outliers final: 5
  residues processed: 28
  average time/residue: 0.0932
  time to fit residues: 4.6066
Evaluate side-chains
  22 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 17
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   68 CYS
Chi-restraints excluded: chain R residue  148 THR
Chi-restraints excluded: chain R residue  166 ASN
Chi-restraints excluded: chain X residue  520 ILE
Chi-restraints excluded: chain X residue  529 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 74 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   chunk 52 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   chunk 1 optimal weight:   10.0000
   chunk 22 optimal weight:    0.8980
   chunk 63 optimal weight:    3.9990
   chunk 7 optimal weight:    7.9990
   chunk 75 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   overall best weight:    1.5184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** R  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.073084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.060123 restraints weight = 90542.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.061689 restraints weight = 39390.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.062579 restraints weight = 23737.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.062622 restraints weight = 17721.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.062934 restraints weight = 17006.150|
|-----------------------------------------------------------------------------|
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7258
moved from start:          0.3249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   6757  Z= 0.213
  Angle     :  0.630   8.502   9242  Z= 0.314
  Chirality :  0.040   0.138   1073
  Planarity :  0.004   0.043   1160
  Dihedral  :  5.225  47.894    871
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 10.86 %
    Favored  : 88.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.47 (0.29), residues: 801
  helix: -1.72 (0.63), residues: 57
  sheet:  1.02 (0.26), residues: 349
  loop :  0.06 (0.32), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG X 457 
 TYR   0.007   0.001   TYR H 256 
 PHE   0.011   0.002   PHE R  84 
 TRP   0.012   0.002   TRP X 407 
 HIS   0.006   0.001   HIS X 316 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00454 /  0.21 ( 6731)
  covalent geometry    : angle       0.58398 /  0.30 ( 9174)
  SS BOND              : bond        0.00406 /  0.21 (   10)
  SS BOND              : angle       2.59913 /  1.30 (   20)
  hydrogen bonds       : bond        0.03184 /  2.19 (  260)
  hydrogen bonds       : angle       5.12888 /  3.71 (  747)
  link_ALPHA1-3        : bond        0.00481 /  0.25 (    2)
  link_ALPHA1-3        : angle       1.39592 /  0.86 (    6)
  link_ALPHA1-4        : bond        0.00285 /  0.15 (    1)
  link_ALPHA1-4        : angle       1.91106 /  1.29 (    3)
  link_ALPHA1-6        : bond        0.00281 /  0.14 (    2)
  link_ALPHA1-6        : angle       1.46137 /  0.97 (    6)
  link_BETA1-4         : bond        0.00435 /  0.23 (    5)
  link_BETA1-4         : angle       1.94591 /  1.16 (   15)
  link_NAG-ASN         : bond        0.00714 /  0.35 (    6)
  link_NAG-ASN         : angle       4.14160 /  2.47 (   18)

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

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

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 17
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 8
  outliers final: 5
  residues processed: 24
  average time/residue: 0.1009
  time to fit residues: 4.2844
Evaluate side-chains
  20 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 15
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   68 CYS
Chi-restraints excluded: chain R residue  148 THR
Chi-restraints excluded: chain R residue  166 ASN
Chi-restraints excluded: chain X residue  520 ILE
Chi-restraints excluded: chain X residue  529 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 67 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 49 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9990
   chunk 60 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   chunk 68 optimal weight:    0.6980
   overall best weight:    0.8182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** R  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.073444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.059024 restraints weight = 89270.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.061309 restraints weight = 37109.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.062722 restraints weight = 20994.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.063482 restraints weight = 14503.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 54)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.064063 restraints weight = 11728.996|
|-----------------------------------------------------------------------------|
r_work (final): 0.3774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7175
moved from start:          0.3343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   6757  Z= 0.129
  Angle     :  0.557   8.453   9242  Z= 0.275
  Chirality :  0.040   0.148   1073
  Planarity :  0.004   0.042   1160
  Dihedral  :  4.886  44.626    871
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  : 11.28 %
    Favored  : 87.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.69 (0.29), residues: 801
  helix: -1.39 (0.65), residues: 56
  sheet:  1.14 (0.26), residues: 342
  loop :  0.23 (0.32), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG X 390 
 TYR   0.008   0.001   TYR X 307 
 PHE   0.007   0.001   PHE X 500 
 TRP   0.013   0.001   TRP X 513 
 HIS   0.003   0.001   HIS X 316 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00281 /  0.13 ( 6731)
  covalent geometry    : angle       0.51797 /  0.27 ( 9174)
  SS BOND              : bond        0.00209 /  0.11 (   10)
  SS BOND              : angle       1.60609 /  0.80 (   20)
  hydrogen bonds       : bond        0.02828 /  1.95 (  260)
  hydrogen bonds       : angle       4.96013 /  3.59 (  747)
  link_ALPHA1-3        : bond        0.00525 /  0.27 (    2)
  link_ALPHA1-3        : angle       1.39202 /  0.86 (    6)
  link_ALPHA1-4        : bond        0.00072 /  0.04 (    1)
  link_ALPHA1-4        : angle       1.68162 /  1.27 (    3)
  link_ALPHA1-6        : bond        0.00325 /  0.16 (    2)
  link_ALPHA1-6        : angle       1.43354 /  0.97 (    6)
  link_BETA1-4         : bond        0.00311 /  0.18 (    5)
  link_BETA1-4         : angle       1.59006 /  0.99 (   15)
  link_NAG-ASN         : bond        0.00549 /  0.27 (    6)
  link_NAG-ASN         : angle       3.99715 /  2.37 (   18)

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

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

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 18
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 6
  outliers final: 4
  residues processed: 23
  average time/residue: 0.0845
  time to fit residues: 3.3645
Evaluate side-chains
  20 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 16
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   68 CYS
Chi-restraints excluded: chain R residue  148 THR
Chi-restraints excluded: chain R residue  166 ASN
Chi-restraints excluded: chain X residue  520 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 64 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9990
   chunk 33 optimal weight:    0.5980
   chunk 19 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 18 optimal weight:    0.5980
   chunk 1 optimal weight:    8.9990
   chunk 49 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 7 optimal weight:    5.9990
   chunk 31 optimal weight:    0.2980
   overall best weight:    0.6582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** R  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.073746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.061057 restraints weight = 89482.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.062408 restraints weight = 37557.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.063342 restraints weight = 23136.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.063420 restraints weight = 17019.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.063728 restraints weight = 16705.384|
|-----------------------------------------------------------------------------|
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7202
moved from start:          0.3515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6757  Z= 0.116
  Angle     :  0.539   8.241   9242  Z= 0.266
  Chirality :  0.040   0.154   1073
  Planarity :  0.004   0.040   1160
  Dihedral  :  4.558  38.114    871
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 11.14 %
    Favored  : 87.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.93 (0.30), residues: 801
  helix: -1.06 (0.67), residues: 56
  sheet:  1.21 (0.26), residues: 342
  loop :  0.46 (0.33), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG X 390 
 TYR   0.012   0.001   TYR X 307 
 PHE   0.006   0.001   PHE X 500 
 TRP   0.015   0.001   TRP X 513 
 HIS   0.002   0.001   HIS X 316 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00258 /  0.12 ( 6731)
  covalent geometry    : angle       0.50044 /  0.26 ( 9174)
  SS BOND              : bond        0.00220 /  0.12 (   10)
  SS BOND              : angle       1.86206 /  1.05 (   20)
  hydrogen bonds       : bond        0.02675 /  1.85 (  260)
  hydrogen bonds       : angle       4.75783 /  3.43 (  747)
  link_ALPHA1-3        : bond        0.00495 /  0.25 (    2)
  link_ALPHA1-3        : angle       1.39791 /  0.88 (    6)
  link_ALPHA1-4        : bond        0.00065 /  0.03 (    1)
  link_ALPHA1-4        : angle       1.56837 /  1.19 (    3)
  link_ALPHA1-6        : bond        0.00363 /  0.18 (    2)
  link_ALPHA1-6        : angle       1.43273 /  0.96 (    6)
  link_BETA1-4         : bond        0.00225 /  0.14 (    5)
  link_BETA1-4         : angle       1.52310 /  0.98 (   15)
  link_NAG-ASN         : bond        0.00505 /  0.25 (    6)
  link_NAG-ASN         : angle       3.77037 /  2.23 (   18)

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

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

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 19
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  106 ARG cc_start: 0.6982 (ptm160) cc_final: 0.6768 (ptm-80)
  outliers start: 7
  outliers final: 6
  residues processed: 25
  average time/residue: 0.1232
  time to fit residues: 4.9975
Evaluate side-chains
  23 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 17
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   68 CYS
Chi-restraints excluded: chain R residue   72 GLN
Chi-restraints excluded: chain R residue  148 THR
Chi-restraints excluded: chain R residue  166 ASN
Chi-restraints excluded: chain X residue  520 ILE
Chi-restraints excluded: chain X residue  529 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 56 optimal weight:    0.9990
   chunk 35 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 58 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 14 optimal weight:    0.8980
   chunk 9 optimal weight:    4.9990
   chunk 28 optimal weight:    4.9990
   chunk 1 optimal weight:    7.9990
   chunk 44 optimal weight:    0.7980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** R  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.073543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.060805 restraints weight = 89035.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.062110 restraints weight = 37885.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.063025 restraints weight = 23600.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.063103 restraints weight = 17255.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.063410 restraints weight = 17116.572|
|-----------------------------------------------------------------------------|
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7233
moved from start:          0.3686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6757  Z= 0.133
  Angle     :  0.562  11.993   9242  Z= 0.277
  Chirality :  0.040   0.147   1073
  Planarity :  0.004   0.041   1160
  Dihedral  :  4.576  34.688    871
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 11.28 %
    Favored  : 87.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.89 (0.30), residues: 801
  helix: -1.14 (0.66), residues: 57
  sheet:  1.14 (0.26), residues: 348
  loop :  0.49 (0.33), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG X 457 
 TYR   0.013   0.001   TYR X 307 
 PHE   0.006   0.001   PHE X 500 
 TRP   0.013   0.001   TRP H 513 
 HIS   0.003   0.001   HIS X 316 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.13 ( 6731)
  covalent geometry    : angle       0.51011 /  0.26 ( 9174)
  SS BOND              : bond        0.00281 /  0.15 (   10)
  SS BOND              : angle       3.29980 /  1.52 (   20)
  hydrogen bonds       : bond        0.02709 /  1.87 (  260)
  hydrogen bonds       : angle       4.75657 /  3.42 (  747)
  link_ALPHA1-3        : bond        0.00506 /  0.26 (    2)
  link_ALPHA1-3        : angle       1.39613 /  0.87 (    6)
  link_ALPHA1-4        : bond        0.00036 /  0.02 (    1)
  link_ALPHA1-4        : angle       1.64066 /  1.20 (    3)
  link_ALPHA1-6        : bond        0.00357 /  0.18 (    2)
  link_ALPHA1-6        : angle       1.43968 /  0.96 (    6)
  link_BETA1-4         : bond        0.00287 /  0.17 (    5)
  link_BETA1-4         : angle       1.56403 /  0.99 (   15)
  link_NAG-ASN         : bond        0.00514 /  0.25 (    6)
  link_NAG-ASN         : angle       3.68446 /  2.20 (   18)

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

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

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 17
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 7
  outliers final: 6
  residues processed: 23
  average time/residue: 0.0973
  time to fit residues: 3.7001
Evaluate side-chains
  23 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 17
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   68 CYS
Chi-restraints excluded: chain R residue   72 GLN
Chi-restraints excluded: chain R residue  148 THR
Chi-restraints excluded: chain R residue  166 ASN
Chi-restraints excluded: chain X residue  520 ILE
Chi-restraints excluded: chain X residue  529 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 72 optimal weight:    0.8980
   chunk 4 optimal weight:    6.9990
   chunk 54 optimal weight:    0.7980
   chunk 9 optimal weight:    4.9990
   chunk 43 optimal weight:    0.7980
   chunk 49 optimal weight:    0.8980
   chunk 56 optimal weight:    8.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** R  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.073348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.058979 restraints weight = 89425.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.061288 restraints weight = 36633.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.062698 restraints weight = 20561.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.063475 restraints weight = 14208.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.063983 restraints weight = 11465.504|
|-----------------------------------------------------------------------------|
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7186
moved from start:          0.3844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6757  Z= 0.131
  Angle     :  0.545   9.225   9242  Z= 0.268
  Chirality :  0.040   0.149   1073
  Planarity :  0.004   0.040   1160
  Dihedral  :  4.450  29.476    871
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  : 11.56 %
    Favored  : 87.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.92 (0.30), residues: 801
  helix: -1.06 (0.66), residues: 57
  sheet:  1.13 (0.26), residues: 348
  loop :  0.52 (0.33), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG X 457 
 TYR   0.016   0.001   TYR X 307 
 PHE   0.007   0.001   PHE X 318 
 TRP   0.012   0.001   TRP H 513 
 HIS   0.003   0.001   HIS X 316 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00287 /  0.13 ( 6731)
  covalent geometry    : angle       0.50137 /  0.26 ( 9174)
  SS BOND              : bond        0.00414 /  0.21 (   10)
  SS BOND              : angle       2.58267 /  1.18 (   20)
  hydrogen bonds       : bond        0.02698 /  1.86 (  260)
  hydrogen bonds       : angle       4.73168 /  3.39 (  747)
  link_ALPHA1-3        : bond        0.00453 /  0.23 (    2)
  link_ALPHA1-3        : angle       1.38387 /  0.86 (    6)
  link_ALPHA1-4        : bond        0.00071 /  0.04 (    1)
  link_ALPHA1-4        : angle       1.65091 /  1.21 (    3)
  link_ALPHA1-6        : bond        0.00339 /  0.17 (    2)
  link_ALPHA1-6        : angle       1.43953 /  0.96 (    6)
  link_BETA1-4         : bond        0.00269 /  0.17 (    5)
  link_BETA1-4         : angle       1.54395 /  0.98 (   15)
  link_NAG-ASN         : bond        0.00517 /  0.26 (    6)
  link_NAG-ASN         : angle       3.60256 /  2.15 (   18)

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

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

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 18
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 6
  outliers final: 5
  residues processed: 23
  average time/residue: 0.1127
  time to fit residues: 3.9948
Evaluate side-chains
  23 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 18
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   72 GLN
Chi-restraints excluded: chain R residue  148 THR
Chi-restraints excluded: chain R residue  166 ASN
Chi-restraints excluded: chain X residue  520 ILE
Chi-restraints excluded: chain X residue  529 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 55 optimal weight:    7.9990
   chunk 6 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   chunk 31 optimal weight:    0.3980
   chunk 4 optimal weight:    4.9990
   chunk 28 optimal weight:    4.9990
   chunk 32 optimal weight:    0.3980
   chunk 48 optimal weight:    5.9990
   overall best weight:    0.7384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
R  71 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.073711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.060093 restraints weight = 89030.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.063051 restraints weight = 33637.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.063342 restraints weight = 17743.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.063567 restraints weight = 16756.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.063840 restraints weight = 13970.208|
|-----------------------------------------------------------------------------|
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7212
moved from start:          0.4054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6757  Z= 0.115
  Angle     :  0.532   7.495   9242  Z= 0.262
  Chirality :  0.040   0.156   1073
  Planarity :  0.004   0.041   1160
  Dihedral  :  4.335  21.699    871
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  : 11.42 %
    Favored  : 87.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.99 (0.30), residues: 801
  helix: -1.01 (0.67), residues: 57
  sheet:  1.20 (0.26), residues: 354
  loop :  0.53 (0.34), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG X 390 
 TYR   0.013   0.001   TYR R  80 
 PHE   0.007   0.001   PHE X 318 
 TRP   0.013   0.001   TRP X 513 
 HIS   0.004   0.001   HIS R  70 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00257 /  0.11 ( 6731)
  covalent geometry    : angle       0.49330 /  0.25 ( 9174)
  SS BOND              : bond        0.00138 /  0.08 (   10)
  SS BOND              : angle       2.11294 /  0.99 (   20)
  hydrogen bonds       : bond        0.02584 /  1.78 (  260)
  hydrogen bonds       : angle       4.64747 /  3.33 (  747)
  link_ALPHA1-3        : bond        0.00488 /  0.25 (    2)
  link_ALPHA1-3        : angle       1.38846 /  0.86 (    6)
  link_ALPHA1-4        : bond        0.00053 /  0.03 (    1)
  link_ALPHA1-4        : angle       1.63930 /  1.24 (    3)
  link_ALPHA1-6        : bond        0.00348 /  0.17 (    2)
  link_ALPHA1-6        : angle       1.43956 /  0.96 (    6)
  link_BETA1-4         : bond        0.00246 /  0.15 (    5)
  link_BETA1-4         : angle       1.47211 /  0.93 (   15)
  link_NAG-ASN         : bond        0.00515 /  0.25 (    6)
  link_NAG-ASN         : angle       3.56297 /  2.11 (   18)

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

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

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 19
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 6
  outliers final: 4
  residues processed: 24
  average time/residue: 0.1214
  time to fit residues: 4.5036
Evaluate side-chains
  23 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 19
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   72 GLN
Chi-restraints excluded: chain R residue  148 THR
Chi-restraints excluded: chain X residue  520 ILE
Chi-restraints excluded: chain X residue  529 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 77 optimal weight:    0.0040
   chunk 41 optimal weight:    2.9990
   chunk 52 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 40 optimal weight:    0.5980
   chunk 22 optimal weight:    0.8980
   chunk 9 optimal weight:    6.9990
   overall best weight:    0.6192

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.073751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.059612 restraints weight = 88631.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.061861 restraints weight = 36929.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.063257 restraints weight = 20937.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.064021 restraints weight = 14552.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.064504 restraints weight = 11769.061|
|-----------------------------------------------------------------------------|
r_work (final): 0.3780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7195
moved from start:          0.4101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   6757  Z= 0.107
  Angle     :  0.521   7.237   9242  Z= 0.256
  Chirality :  0.040   0.157   1073
  Planarity :  0.004   0.041   1160
  Dihedral  :  4.220  19.188    871
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 11.42 %
    Favored  : 87.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.01 (0.30), residues: 801
  helix: -0.96 (0.67), residues: 57
  sheet:  1.22 (0.26), residues: 355
  loop :  0.53 (0.34), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG X 437 
 TYR   0.012   0.001   TYR X 307 
 PHE   0.006   0.001   PHE X 318 
 TRP   0.014   0.001   TRP X 513 
 HIS   0.002   0.001   HIS X 316 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00242 /  0.11 ( 6731)
  covalent geometry    : angle       0.48458 /  0.25 ( 9174)
  SS BOND              : bond        0.00119 /  0.07 (   10)
  SS BOND              : angle       1.97905 /  0.92 (   20)
  hydrogen bonds       : bond        0.02539 /  1.75 (  260)
  hydrogen bonds       : angle       4.60178 /  3.29 (  747)
  link_ALPHA1-3        : bond        0.00477 /  0.24 (    2)
  link_ALPHA1-3        : angle       1.38714 /  0.87 (    6)
  link_ALPHA1-4        : bond        0.00009 /  0.00 (    1)
  link_ALPHA1-4        : angle       1.63314 /  1.23 (    3)
  link_ALPHA1-6        : bond        0.00353 /  0.18 (    2)
  link_ALPHA1-6        : angle       1.43345 /  0.95 (    6)
  link_BETA1-4         : bond        0.00234 /  0.14 (    5)
  link_BETA1-4         : angle       1.45697 /  0.93 (   15)
  link_NAG-ASN         : bond        0.00483 /  0.24 (    6)
  link_NAG-ASN         : angle       3.42433 /  2.04 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2026.02 seconds
wall clock time: 35 minutes 20.84 seconds (2120.84 seconds total)