Starting phenix.real_space_refine
on Thu May 15 09:06:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8c1b_16377/05_2025/8c1b_16377.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8c1b_16377/05_2025/8c1b_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8c1b_16377/05_2025/8c1b_16377.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8c1b_16377/05_2025/8c1b_16377.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8c1b_16377/05_2025/8c1b_16377.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8c1b_16377/05_2025/8c1b_16377.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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 dihedrals: 15
          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 dihedrals: 9
          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 dihedrals: 15
          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 dihedrals: 9
          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: 7.86, per 1000 atoms: 0.62
  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: 3.38
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 1.27
  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: 4.76

  Time building geometry restraints manager: 4.03 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 -    22.05: 5853
       22.05 -    44.10: 402
       44.10 -    66.15: 84
       66.15 -    88.20: 27
       88.20 -   110.26: 10
  Dihedral angle restraints: 6376
    sinusoidal: 3601
      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 6373 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:             3.770
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.230
  Extract box with map and model:          0.510
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     31.560
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7016
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  : 16.551 110.256   2703
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.06 (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
 TRP   0.035   0.004   TRP R  13 
 HIS   0.013   0.003   HIS H 381 
 PHE   0.021   0.003   PHE X 318 
 TYR   0.021   0.003   TYR R  80 
 ARG   0.015   0.001   ARG R 106 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01119 (    6)
  link_NAG-ASN         : angle      11.11506 (   18)
  link_ALPHA1-4        : bond        0.00467 (    1)
  link_ALPHA1-4        : angle       1.27286 (    3)
  link_ALPHA1-6        : bond        0.00406 (    2)
  link_ALPHA1-6        : angle       1.57731 (    6)
  link_BETA1-4         : bond        0.00377 (    5)
  link_BETA1-4         : angle       2.48239 (   15)
  link_ALPHA1-3        : bond        0.00490 (    2)
  link_ALPHA1-3        : angle       1.51056 (    6)
  hydrogen bonds       : bond        0.10524 (  260)
  hydrogen bonds       : angle       6.95266 (  747)
  SS BOND              : bond        0.01230 (   10)
  SS BOND              : angle       4.43173 (   20)
  covalent geometry    : bond        0.00738 ( 6731)
  covalent geometry    : angle       1.30665 ( 9174)

*********************** 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  : 1.107 
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: 0.3303
  time to fit residues: 12.8443
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  : 1.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 59 optimal weight:    0.4980
   chunk 32 optimal weight:    0.6980
   chunk 20 optimal weight:    2.9990
   chunk 39 optimal weight:    0.6980
   chunk 31 optimal weight:    0.5980
   chunk 61 optimal weight:    0.3980
   chunk 23 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4227 r_free = 0.4227 target = 0.081313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.069024 restraints weight = 107706.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.071073 restraints weight = 49977.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.072294 restraints weight = 30224.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.4017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6989
moved from start:          0.0932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6757  Z= 0.124
  Angle     :  0.655   8.807   9242  Z= 0.327
  Chirality :  0.043   0.167   1073
  Planarity :  0.005   0.066   1160
  Dihedral  : 10.974  74.392   1193
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  8.91 %
    Favored  : 89.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.29), residues: 801
  helix: -1.51 (0.58), residues: 57
  sheet:  1.21 (0.26), residues: 377
  loop : -0.06 (0.33), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP X 513 
 HIS   0.004   0.001   HIS R 134 
 PHE   0.007   0.001   PHE X 500 
 TYR   0.005   0.001   TYR H 307 
 ARG   0.002   0.000   ARG X 486 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00466 (    6)
  link_NAG-ASN         : angle       4.48619 (   18)
  link_ALPHA1-4        : bond        0.01094 (    1)
  link_ALPHA1-4        : angle       1.52094 (    3)
  link_ALPHA1-6        : bond        0.00800 (    2)
  link_ALPHA1-6        : angle       2.31276 (    6)
  link_BETA1-4         : bond        0.00373 (    5)
  link_BETA1-4         : angle       2.21181 (   15)
  link_ALPHA1-3        : bond        0.00816 (    2)
  link_ALPHA1-3        : angle       2.49839 (    6)
  hydrogen bonds       : bond        0.03684 (  260)
  hydrogen bonds       : angle       5.58711 (  747)
  SS BOND              : bond        0.00429 (   10)
  SS BOND              : angle       1.37202 (   20)
  covalent geometry    : bond        0.00267 ( 6731)
  covalent geometry    : angle       0.60994 ( 9174)

*********************** 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: 8
    poor density    : 21
  time to evaluate  : 0.989 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 8
  outliers final: 3
  residues processed: 28
  average time/residue: 0.2500
  time to fit residues: 11.5744
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  : 0.970 
-------------------------------------------------------------------------------
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 52 optimal weight:    2.9990
   chunk 19 optimal weight:    4.9990
   chunk 5 optimal weight:    9.9990
   chunk 17 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 50 optimal weight:    0.0670
   chunk 77 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 40 optimal weight:    0.6980
   chunk 7 optimal weight:    6.9990
   overall best weight:    1.1524

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

Flipped N/Q/H residues before XYZ refinement:
H 381 HIS
** H 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.075604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.062079 restraints weight = 99858.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.064373 restraints weight = 41479.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.065726 restraints weight = 23522.691|
|-----------------------------------------------------------------------------|
r_work (final): 0.3828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7191
moved from start:          0.1822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6757  Z= 0.181
  Angle     :  0.639   8.176   9242  Z= 0.315
  Chirality :  0.042   0.192   1073
  Planarity :  0.005   0.048   1160
  Dihedral  :  7.858  49.353   1193
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  8.77 %
    Favored  : 90.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.29), residues: 801
  helix: -1.55 (0.60), residues: 58
  sheet:  1.49 (0.26), residues: 347
  loop :  0.23 (0.32), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP H 513 
 HIS   0.005   0.001   HIS X 316 
 PHE   0.009   0.001   PHE H 445 
 TYR   0.009   0.001   TYR R 149 
 ARG   0.007   0.001   ARG X 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00654 (    6)
  link_NAG-ASN         : angle       4.28860 (   18)
  link_ALPHA1-4        : bond        0.00173 (    1)
  link_ALPHA1-4        : angle       1.91106 (    3)
  link_ALPHA1-6        : bond        0.00871 (    2)
  link_ALPHA1-6        : angle       2.25687 (    6)
  link_BETA1-4         : bond        0.00482 (    5)
  link_BETA1-4         : angle       2.24847 (   15)
  link_ALPHA1-3        : bond        0.01278 (    2)
  link_ALPHA1-3        : angle       2.16875 (    6)
  hydrogen bonds       : bond        0.03165 (  260)
  hydrogen bonds       : angle       5.01389 (  747)
  SS BOND              : bond        0.00447 (   10)
  SS BOND              : angle       1.86456 (   20)
  covalent geometry    : bond        0.00379 ( 6731)
  covalent geometry    : angle       0.59336 ( 9174)

*********************** 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  : 0.955 
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: 8
  outliers final: 3
  residues processed: 28
  average time/residue: 0.2852
  time to fit residues: 12.5978
Evaluate side-chains
  19 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 16
  time to evaluate  : 1.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 53 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   chunk 47 optimal weight:    5.9990
   chunk 14 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 5 optimal weight:    9.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
** H 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3992 r_free = 0.3992 target = 0.073199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.059604 restraints weight = 94200.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.061269 restraints weight = 39142.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.062280 restraints weight = 24956.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.3684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7329
moved from start:          0.2814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048   6757  Z= 0.273
  Angle     :  0.703   8.268   9242  Z= 0.349
  Chirality :  0.042   0.138   1073
  Planarity :  0.005   0.046   1160
  Dihedral  :  6.823  52.721   1193
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  :  9.89 %
    Favored  : 88.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.29), residues: 801
  helix: -1.93 (0.59), residues: 58
  sheet:  1.13 (0.26), residues: 347
  loop :  0.01 (0.32), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP H 407 
 HIS   0.008   0.002   HIS H 477 
 PHE   0.014   0.002   PHE H 445 
 TYR   0.020   0.002   TYR X 307 
 ARG   0.009   0.001   ARG X 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00824 (    6)
  link_NAG-ASN         : angle       4.27409 (   18)
  link_ALPHA1-4        : bond        0.00204 (    1)
  link_ALPHA1-4        : angle       2.09933 (    3)
  link_ALPHA1-6        : bond        0.00438 (    2)
  link_ALPHA1-6        : angle       2.05781 (    6)
  link_BETA1-4         : bond        0.00668 (    5)
  link_BETA1-4         : angle       2.43794 (   15)
  link_ALPHA1-3        : bond        0.00876 (    2)
  link_ALPHA1-3        : angle       2.57192 (    6)
  hydrogen bonds       : bond        0.03601 (  260)
  hydrogen bonds       : angle       5.29996 (  747)
  SS BOND              : bond        0.00473 (   10)
  SS BOND              : angle       2.14245 (   20)
  covalent geometry    : bond        0.00572 ( 6731)
  covalent geometry    : angle       0.65815 ( 9174)

*********************** 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
  26 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 17
  time to evaluate  : 1.147 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 9
  outliers final: 5
  residues processed: 25
  average time/residue: 0.2432
  time to fit residues: 10.6947
Evaluate side-chains
  19 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 14
  time to evaluate  : 1.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   49 THR
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 32 optimal weight:    0.5980
   chunk 11 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 39 optimal weight:    2.9990
   chunk 70 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 76 optimal weight:    0.8980
   chunk 31 optimal weight:    0.1980
   chunk 36 optimal weight:    0.6980
   chunk 4 optimal weight:    5.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** H 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4037 r_free = 0.4037 target = 0.074628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.061891 restraints weight = 88818.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.063297 restraints weight = 37195.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.064248 restraints weight = 22359.150|
|-----------------------------------------------------------------------------|
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7247
moved from start:          0.2811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   6757  Z= 0.114
  Angle     :  0.571   8.344   9242  Z= 0.281
  Chirality :  0.041   0.152   1073
  Planarity :  0.004   0.043   1160
  Dihedral  :  6.209  49.772   1193
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 10.45 %
    Favored  : 88.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.29), residues: 801
  helix: -1.56 (0.63), residues: 57
  sheet:  1.19 (0.26), residues: 343
  loop :  0.24 (0.32), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP H 513 
 HIS   0.002   0.001   HIS X 316 
 PHE   0.007   0.001   PHE X 501 
 TYR   0.006   0.001   TYR X 307 
 ARG   0.003   0.000   ARG X 390 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00545 (    6)
  link_NAG-ASN         : angle       4.13507 (   18)
  link_ALPHA1-4        : bond        0.00085 (    1)
  link_ALPHA1-4        : angle       1.73223 (    3)
  link_ALPHA1-6        : bond        0.00309 (    2)
  link_ALPHA1-6        : angle       1.66750 (    6)
  link_BETA1-4         : bond        0.00264 (    5)
  link_BETA1-4         : angle       1.77067 (   15)
  link_ALPHA1-3        : bond        0.01102 (    2)
  link_ALPHA1-3        : angle       1.99449 (    6)
  hydrogen bonds       : bond        0.02888 (  260)
  hydrogen bonds       : angle       4.96776 (  747)
  SS BOND              : bond        0.00223 (   10)
  SS BOND              : angle       1.88805 (   20)
  covalent geometry    : bond        0.00249 ( 6731)
  covalent geometry    : angle       0.52575 ( 9174)

*********************** 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
  23 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 16
  time to evaluate  : 1.083 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 7
  outliers final: 4
  residues processed: 22
  average time/residue: 0.2403
  time to fit residues: 9.4405
Evaluate side-chains
  19 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 15
  time to evaluate  : 1.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 52 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 14 optimal weight:    2.9990
   chunk 45 optimal weight:    0.4980
   chunk 50 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 34 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   chunk 48 optimal weight:    7.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
** H 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.073326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.060043 restraints weight = 90538.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.061973 restraints weight = 37972.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.062756 restraints weight = 21976.884|
|-----------------------------------------------------------------------------|
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7294
moved from start:          0.3309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6757  Z= 0.183
  Angle     :  0.597   8.248   9242  Z= 0.296
  Chirality :  0.040   0.134   1073
  Planarity :  0.004   0.041   1160
  Dihedral  :  5.917  50.666   1193
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 10.58 %
    Favored  : 88.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.29), residues: 801
  helix: -1.49 (0.65), residues: 57
  sheet:  0.98 (0.25), residues: 348
  loop :  0.27 (0.33), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP H 513 
 HIS   0.005   0.001   HIS X 316 
 PHE   0.011   0.001   PHE R  84 
 TYR   0.014   0.001   TYR X 307 
 ARG   0.006   0.001   ARG X 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00682 (    6)
  link_NAG-ASN         : angle       4.02262 (   18)
  link_ALPHA1-4        : bond        0.00154 (    1)
  link_ALPHA1-4        : angle       1.84383 (    3)
  link_ALPHA1-6        : bond        0.00311 (    2)
  link_ALPHA1-6        : angle       1.50843 (    6)
  link_BETA1-4         : bond        0.00401 (    5)
  link_BETA1-4         : angle       1.81396 (   15)
  link_ALPHA1-3        : bond        0.00877 (    2)
  link_ALPHA1-3        : angle       1.83396 (    6)
  hydrogen bonds       : bond        0.03037 (  260)
  hydrogen bonds       : angle       4.96988 (  747)
  SS BOND              : bond        0.00445 (   10)
  SS BOND              : angle       2.40127 (   20)
  covalent geometry    : bond        0.00390 ( 6731)
  covalent geometry    : angle       0.55204 ( 9174)

*********************** 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
  25 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 16
  time to evaluate  : 0.980 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   37 THR cc_start: 0.6396 (OUTLIER) cc_final: 0.6155 (p)
  outliers start: 9
  outliers final: 5
  residues processed: 24
  average time/residue: 0.2245
  time to fit residues: 9.6578
Evaluate side-chains
  20 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 14
  time to evaluate  : 1.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   37 THR
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 57 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9990
   chunk 50 optimal weight:    0.0870
   chunk 32 optimal weight:    0.6980
   chunk 75 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 69 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.8962

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

Flipped N/Q/H residues before XYZ refinement:
** H 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3996 r_free = 0.3996 target = 0.073475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.059676 restraints weight = 93540.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.062243 restraints weight = 39890.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.062566 restraints weight = 22773.232|
|-----------------------------------------------------------------------------|
r_work (final): 0.3697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7298
moved from start:          0.3472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6757  Z= 0.128
  Angle     :  0.563   9.182   9242  Z= 0.278
  Chirality :  0.040   0.151   1073
  Planarity :  0.004   0.041   1160
  Dihedral  :  5.593  48.341   1193
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 10.58 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.79 (0.29), residues: 801
  helix: -1.33 (0.65), residues: 57
  sheet:  1.11 (0.26), residues: 341
  loop :  0.42 (0.33), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP X 513 
 HIS   0.003   0.001   HIS X 316 
 PHE   0.006   0.001   PHE X 500 
 TYR   0.010   0.001   TYR X 307 
 ARG   0.003   0.000   ARG X 390 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00532 (    6)
  link_NAG-ASN         : angle       3.94492 (   18)
  link_ALPHA1-4        : bond        0.00067 (    1)
  link_ALPHA1-4        : angle       1.67213 (    3)
  link_ALPHA1-6        : bond        0.00355 (    2)
  link_ALPHA1-6        : angle       1.50834 (    6)
  link_BETA1-4         : bond        0.00236 (    5)
  link_BETA1-4         : angle       1.60429 (   15)
  link_ALPHA1-3        : bond        0.00859 (    2)
  link_ALPHA1-3        : angle       1.62446 (    6)
  hydrogen bonds       : bond        0.02762 (  260)
  hydrogen bonds       : angle       4.87200 (  747)
  SS BOND              : bond        0.00350 (   10)
  SS BOND              : angle       2.71969 (   20)
  covalent geometry    : bond        0.00279 ( 6731)
  covalent geometry    : angle       0.51357 ( 9174)

*********************** 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
  27 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 20
  time to evaluate  : 1.057 
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: 26
  average time/residue: 0.2391
  time to fit residues: 10.7380
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  : 1.096 
-------------------------------------------------------------------------------
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 15 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 59 optimal weight:    0.5980
   chunk 42 optimal weight:    0.5980
   chunk 71 optimal weight:    0.5980
   chunk 14 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 5 optimal weight:    9.9990
   chunk 20 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** H 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3979 r_free = 0.3979 target = 0.072815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.058069 restraints weight = 93982.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.060448 restraints weight = 37832.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.061914 restraints weight = 21169.716|
|-----------------------------------------------------------------------------|
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7286
moved from start:          0.3643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6757  Z= 0.145
  Angle     :  0.560   7.894   9242  Z= 0.276
  Chirality :  0.040   0.142   1073
  Planarity :  0.004   0.040   1160
  Dihedral  :  5.469  48.612   1193
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  : 11.14 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.30), residues: 801
  helix: -1.19 (0.66), residues: 57
  sheet:  1.01 (0.26), residues: 347
  loop :  0.47 (0.33), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP X 513 
 HIS   0.003   0.001   HIS X 316 
 PHE   0.006   0.001   PHE X 500 
 TYR   0.026   0.001   TYR X 307 
 ARG   0.003   0.000   ARG X 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00539 (    6)
  link_NAG-ASN         : angle       3.84509 (   18)
  link_ALPHA1-4        : bond        0.00084 (    1)
  link_ALPHA1-4        : angle       1.67209 (    3)
  link_ALPHA1-6        : bond        0.00343 (    2)
  link_ALPHA1-6        : angle       1.48463 (    6)
  link_BETA1-4         : bond        0.00303 (    5)
  link_BETA1-4         : angle       1.61632 (   15)
  link_ALPHA1-3        : bond        0.00778 (    2)
  link_ALPHA1-3        : angle       1.59889 (    6)
  hydrogen bonds       : bond        0.02781 (  260)
  hydrogen bonds       : angle       4.83490 (  747)
  SS BOND              : bond        0.00371 (   10)
  SS BOND              : angle       2.33620 (   20)
  covalent geometry    : bond        0.00317 ( 6731)
  covalent geometry    : angle       0.51630 ( 9174)

*********************** 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
  22 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 16
  time to evaluate  : 1.096 
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: 6
  outliers final: 6
  residues processed: 21
  average time/residue: 0.2437
  time to fit residues: 9.3152
Evaluate side-chains
  22 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 16
  time to evaluate  : 1.064 
-------------------------------------------------------------------------------
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 57 optimal weight:    0.9980
   chunk 77 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 0 optimal weight:    5.9990
   chunk 8 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9980
   chunk 46 optimal weight:    2.9990
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
** H 389 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 = 0.3978 r_free = 0.3978 target = 0.072768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.057997 restraints weight = 93362.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.060376 restraints weight = 37628.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.061824 restraints weight = 21089.379|
|-----------------------------------------------------------------------------|
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7290
moved from start:          0.3922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   6757  Z= 0.136
  Angle     :  0.542   7.578   9242  Z= 0.268
  Chirality :  0.040   0.153   1073
  Planarity :  0.004   0.041   1160
  Dihedral  :  5.263  47.406   1193
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 11.14 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.30), residues: 801
  helix: -1.16 (0.65), residues: 57
  sheet:  1.06 (0.26), residues: 344
  loop :  0.48 (0.33), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP X 513 
 HIS   0.003   0.001   HIS H 525 
 PHE   0.007   0.001   PHE X 318 
 TYR   0.012   0.001   TYR R  80 
 ARG   0.003   0.000   ARG X 437 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00533 (    6)
  link_NAG-ASN         : angle       3.73097 (   18)
  link_ALPHA1-4        : bond        0.00135 (    1)
  link_ALPHA1-4        : angle       1.70453 (    3)
  link_ALPHA1-6        : bond        0.00375 (    2)
  link_ALPHA1-6        : angle       1.46011 (    6)
  link_BETA1-4         : bond        0.00264 (    5)
  link_BETA1-4         : angle       1.50420 (   15)
  link_ALPHA1-3        : bond        0.00742 (    2)
  link_ALPHA1-3        : angle       1.44543 (    6)
  hydrogen bonds       : bond        0.02719 (  260)
  hydrogen bonds       : angle       4.81060 (  747)
  SS BOND              : bond        0.00155 (   10)
  SS BOND              : angle       1.78583 (   20)
  covalent geometry    : bond        0.00296 ( 6731)
  covalent geometry    : angle       0.50377 ( 9174)

*********************** 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
  26 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 18
  time to evaluate  : 0.993 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   37 THR cc_start: 0.6601 (OUTLIER) cc_final: 0.6378 (p)
  outliers start: 8
  outliers final: 6
  residues processed: 25
  average time/residue: 0.3020
  time to fit residues: 11.9525
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  : 1.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   37 THR
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 63 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 76 optimal weight:    0.8980
   chunk 40 optimal weight:    0.7980
   chunk 36 optimal weight:    0.5980
   chunk 59 optimal weight:    0.8980
   chunk 77 optimal weight:    0.3980
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** H 389 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 = 0.3985 r_free = 0.3985 target = 0.073088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.058198 restraints weight = 94269.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.060604 restraints weight = 38192.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.062069 restraints weight = 21465.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.3704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7293
moved from start:          0.3980

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= 0.118
  Angle     :  0.544   8.487   9242  Z= 0.268
  Chirality :  0.040   0.155   1073
  Planarity :  0.004   0.040   1160
  Dihedral  :  5.169  46.901   1193
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 5.62
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.30), residues: 801
  helix: -1.06 (0.66), residues: 57
  sheet:  1.13 (0.26), residues: 350
  loop :  0.50 (0.33), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP X 513 
 HIS   0.004   0.001   HIS R 108 
 PHE   0.006   0.001   PHE X 318 
 TYR   0.008   0.001   TYR X 307 
 ARG   0.004   0.000   ARG R 106 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00487 (    6)
  link_NAG-ASN         : angle       3.70250 (   18)
  link_ALPHA1-4        : bond        0.00096 (    1)
  link_ALPHA1-4        : angle       1.69837 (    3)
  link_ALPHA1-6        : bond        0.00374 (    2)
  link_ALPHA1-6        : angle       1.47225 (    6)
  link_BETA1-4         : bond        0.00252 (    5)
  link_BETA1-4         : angle       1.48756 (   15)
  link_ALPHA1-3        : bond        0.00703 (    2)
  link_ALPHA1-3        : angle       1.48655 (    6)
  hydrogen bonds       : bond        0.02637 (  260)
  hydrogen bonds       : angle       4.74191 (  747)
  SS BOND              : bond        0.00346 (   10)
  SS BOND              : angle       2.58973 (   20)
  covalent geometry    : bond        0.00265 ( 6731)
  covalent geometry    : angle       0.49954 ( 9174)

********************** 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
  24 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 17
  time to evaluate  : 0.980 
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: 7
  outliers final: 5
  residues processed: 23
  average time/residue: 0.2411
  time to fit residues: 9.7377
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  : 0.982 
-------------------------------------------------------------------------------
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 35 optimal weight:    0.3980
   chunk 42 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0870
   chunk 32 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 73 optimal weight:    0.8980
   chunk 69 optimal weight:    0.5980
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
** H 389 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 = 0.4018 r_free = 0.4018 target = 0.073986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.059432 restraints weight = 88123.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.061812 restraints weight = 35036.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.063280 restraints weight = 19348.802|
|-----------------------------------------------------------------------------|
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7264
moved from start:          0.4056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6757  Z= 0.102
  Angle     :  0.525   7.528   9242  Z= 0.258
  Chirality :  0.040   0.164   1073
  Planarity :  0.004   0.040   1160
  Dihedral  :  4.954  45.150   1193
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.30), residues: 801
  helix: -0.91 (0.68), residues: 56
  sheet:  1.20 (0.26), residues: 350
  loop :  0.57 (0.33), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP X 513 
 HIS   0.003   0.001   HIS H 477 
 PHE   0.006   0.001   PHE X 318 
 TYR   0.021   0.001   TYR X 307 
 ARG   0.003   0.000   ARG R 106 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00465 (    6)
  link_NAG-ASN         : angle       3.62782 (   18)
  link_ALPHA1-4        : bond        0.00033 (    1)
  link_ALPHA1-4        : angle       1.59707 (    3)
  link_ALPHA1-6        : bond        0.00397 (    2)
  link_ALPHA1-6        : angle       1.46906 (    6)
  link_BETA1-4         : bond        0.00248 (    5)
  link_BETA1-4         : angle       1.43940 (   15)
  link_ALPHA1-3        : bond        0.00685 (    2)
  link_ALPHA1-3        : angle       1.44939 (    6)
  hydrogen bonds       : bond        0.02520 (  260)
  hydrogen bonds       : angle       4.65748 (  747)
  SS BOND              : bond        0.00298 (   10)
  SS BOND              : angle       2.22490 (   20)
  covalent geometry    : bond        0.00230 ( 6731)
  covalent geometry    : angle       0.48417 ( 9174)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4218.91 seconds
wall clock time: 73 minutes 42.54 seconds (4422.54 seconds total)