Starting phenix.real_space_refine
on Wed Jun 11 15:32:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8c1b_16377/06_2025/8c1b_16377.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8c1b_16377/06_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_16377/06_2025/8c1b_16377.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8c1b_16377/06_2025/8c1b_16377.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8c1b_16377/06_2025/8c1b_16377.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8c1b_16377/06_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-5710/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: 7.17, per 1000 atoms: 0.57
  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: 3.60
  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: 1.18
  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: 4.34

  Time building geometry restraints manager: 4.30 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:             5.270
  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:          0.470
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     30.780
  Find NCS groups from input model:        0.190
  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:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.130
-------------------------------------------------------------------------------
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  : 1.067 
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: 0.3338
  time to fit residues: 12.8571
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  : 0.943 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 45 optimal weight:    1.9990
   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 = 56)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.069021 restraints weight = 107706.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.071047 restraints weight = 50070.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.072284 restraints weight = 30159.256|
|-----------------------------------------------------------------------------|
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  : 1.027 
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: 0.2558
  time to fit residues: 11.7706
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  : 0.940 
-------------------------------------------------------------------------------
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:    0.8980
   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:    0.5980
   chunk 7 optimal weight:    6.9990
   overall best weight:    1.1122

-------------------------------------------------------------------------------
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 = 0.4099 r_free = 0.4099 target = 0.076026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.062510 restraints weight = 99962.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.064849 restraints weight = 40588.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.066248 restraints weight = 22773.348|
|-----------------------------------------------------------------------------|
r_work (final): 0.3843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7175
moved from start:          0.1720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6757  Z= 0.172
  Angle     :  0.632   8.390   9242  Z= 0.311
  Chirality :  0.041   0.161   1073
  Planarity :  0.004   0.048   1160
  Dihedral  :  8.055  48.522   1193
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  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:  0.99 (0.30), residues: 801
  helix: -1.52 (0.60), residues: 58
  sheet:  1.40 (0.26), residues: 367
  loop :  0.36 (0.33), residues: 376

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   0.010   0.001   PHE H 500 
 TYR   0.008   0.001   TYR R 149 
 ARG   0.006   0.000   ARG X 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00603 (    6)
  link_NAG-ASN         : angle       4.32393 (   18)
  link_ALPHA1-4        : bond        0.00180 (    1)
  link_ALPHA1-4        : angle       1.82223 (    3)
  link_ALPHA1-6        : bond        0.00801 (    2)
  link_ALPHA1-6        : angle       1.93584 (    6)
  link_BETA1-4         : bond        0.00485 (    5)
  link_BETA1-4         : angle       2.24945 (   15)
  link_ALPHA1-3        : bond        0.01275 (    2)
  link_ALPHA1-3        : angle       2.05300 (    6)
  hydrogen bonds       : bond        0.03176 (  260)
  hydrogen bonds       : angle       5.02894 (  747)
  SS BOND              : bond        0.00457 (   10)
  SS BOND              : angle       1.86872 (   20)
  covalent geometry    : bond        0.00363 ( 6731)
  covalent geometry    : angle       0.58603 ( 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  : 1.066 
Fit side-chains
   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: 0.2965
  time to fit residues: 13.1683
Evaluate side-chains
  21 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 18
  time to evaluate  : 1.088 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 24 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 55 optimal weight:    7.9990
   chunk 44 optimal weight:    0.9980
   chunk 47 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 5 optimal weight:    9.9990
   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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.075716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.062214 restraints weight = 99015.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.064418 restraints weight = 42416.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.065770 restraints weight = 24497.798|
|-----------------------------------------------------------------------------|
r_work (final): 0.3855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7198
moved from start:          0.2128

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= 0.139
  Angle     :  0.580   7.797   9242  Z= 0.284
  Chirality :  0.041   0.148   1073
  Planarity :  0.004   0.045   1160
  Dihedral  :  6.569  48.501   1193
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  :  9.19 %
    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 (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 (0.29), residues: 801
  helix: -1.44 (0.61), residues: 58
  sheet:  1.50 (0.26), residues: 345
  loop :  0.35 (0.32), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H 513 
 HIS   0.004   0.001   HIS H 477 
 PHE   0.008   0.001   PHE X 501 
 TYR   0.011   0.001   TYR X 307 
 ARG   0.004   0.000   ARG X 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00518 (    6)
  link_NAG-ASN         : angle       4.02964 (   18)
  link_ALPHA1-4        : bond        0.00220 (    1)
  link_ALPHA1-4        : angle       1.67313 (    3)
  link_ALPHA1-6        : bond        0.00315 (    2)
  link_ALPHA1-6        : angle       1.97699 (    6)
  link_BETA1-4         : bond        0.00303 (    5)
  link_BETA1-4         : angle       1.94772 (   15)
  link_ALPHA1-3        : bond        0.01091 (    2)
  link_ALPHA1-3        : angle       2.42150 (    6)
  hydrogen bonds       : bond        0.02964 (  260)
  hydrogen bonds       : angle       4.85669 (  747)
  SS BOND              : bond        0.00402 (   10)
  SS BOND              : angle       1.72404 (   20)
  covalent geometry    : bond        0.00296 ( 6731)
  covalent geometry    : angle       0.53578 ( 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
  24 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 17
  time to evaluate  : 1.061 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 7
  outliers final: 4
  residues processed: 23
  average time/residue: 0.2475
  time to fit residues: 10.0312
Evaluate side-chains
  21 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 17
  time to evaluate  : 1.057 
-------------------------------------------------------------------------------
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0370
   chunk 11 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 24 optimal weight:    0.8980
   chunk 76 optimal weight:    0.7980
   chunk 31 optimal weight:    0.4980
   chunk 36 optimal weight:    0.6980
   chunk 4 optimal weight:    5.9990
   overall best weight:    0.5858

-------------------------------------------------------------------------------
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 = 0.4105 r_free = 0.4105 target = 0.076331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.062542 restraints weight = 102003.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.064829 restraints weight = 42926.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.066225 restraints weight = 24859.320|
|-----------------------------------------------------------------------------|
r_work (final): 0.3836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7209
moved from start:          0.2412

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= 0.106
  Angle     :  0.547   7.266   9242  Z= 0.268
  Chirality :  0.041   0.155   1073
  Planarity :  0.004   0.043   1160
  Dihedral  :  5.858  47.810   1193
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  :  9.61 %
    Favored  : 89.42 %
  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:  1.20 (0.29), residues: 801
  helix: -1.18 (0.63), residues: 57
  sheet:  1.47 (0.25), residues: 354
  loop :  0.59 (0.33), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP H 513 
 HIS   0.003   0.001   HIS X 316 
 PHE   0.006   0.001   PHE X 501 
 TYR   0.005   0.001   TYR X 307 
 ARG   0.003   0.000   ARG X 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00477 (    6)
  link_NAG-ASN         : angle       3.81022 (   18)
  link_ALPHA1-4        : bond        0.00264 (    1)
  link_ALPHA1-4        : angle       1.62915 (    3)
  link_ALPHA1-6        : bond        0.00348 (    2)
  link_ALPHA1-6        : angle       1.66512 (    6)
  link_BETA1-4         : bond        0.00255 (    5)
  link_BETA1-4         : angle       1.68715 (   15)
  link_ALPHA1-3        : bond        0.01027 (    2)
  link_ALPHA1-3        : angle       1.86520 (    6)
  hydrogen bonds       : bond        0.02715 (  260)
  hydrogen bonds       : angle       4.60571 (  747)
  SS BOND              : bond        0.00265 (   10)
  SS BOND              : angle       1.87811 (   20)
  covalent geometry    : bond        0.00233 ( 6731)
  covalent geometry    : angle       0.50604 ( 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
  26 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 19
  time to evaluate  : 0.972 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 7
  outliers final: 3
  residues processed: 25
  average time/residue: 0.2379
  time to fit residues: 10.2597
Evaluate side-chains
  20 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 17
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 52 optimal weight:    0.7980
   chunk 64 optimal weight:    3.9990
   chunk 32 optimal weight:    0.5980
   chunk 14 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9980
   chunk 50 optimal weight:    0.0870
   chunk 0 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 48 optimal weight:    6.9990
   overall best weight:    0.8960

-------------------------------------------------------------------------------
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 = 0.4034 r_free = 0.4034 target = 0.074792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.061284 restraints weight = 93823.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.063422 restraints weight = 38814.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.064137 restraints weight = 22648.086|
|-----------------------------------------------------------------------------|
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7240
moved from start:          0.2744

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= 0.143
  Angle     :  0.553   6.869   9242  Z= 0.272
  Chirality :  0.040   0.140   1073
  Planarity :  0.004   0.043   1160
  Dihedral  :  5.544  48.280   1193
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  9.89 %
    Favored  : 89.42 %
  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:  1.11 (0.30), residues: 801
  helix: -1.11 (0.64), residues: 57
  sheet:  1.39 (0.26), residues: 355
  loop :  0.52 (0.33), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H 513 
 HIS   0.004   0.001   HIS X 316 
 PHE   0.006   0.001   PHE X 500 
 TYR   0.012   0.001   TYR X 307 
 ARG   0.005   0.000   ARG X 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00525 (    6)
  link_NAG-ASN         : angle       3.64809 (   18)
  link_ALPHA1-4        : bond        0.00108 (    1)
  link_ALPHA1-4        : angle       1.64596 (    3)
  link_ALPHA1-6        : bond        0.00298 (    2)
  link_ALPHA1-6        : angle       1.54169 (    6)
  link_BETA1-4         : bond        0.00316 (    5)
  link_BETA1-4         : angle       1.77226 (   15)
  link_ALPHA1-3        : bond        0.00866 (    2)
  link_ALPHA1-3        : angle       1.86797 (    6)
  hydrogen bonds       : bond        0.02746 (  260)
  hydrogen bonds       : angle       4.62015 (  747)
  SS BOND              : bond        0.00381 (   10)
  SS BOND              : angle       2.06015 (   20)
  covalent geometry    : bond        0.00312 ( 6731)
  covalent geometry    : angle       0.51236 ( 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
  23 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 18
  time to evaluate  : 0.991 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 5
  outliers final: 3
  residues processed: 22
  average time/residue: 0.2510
  time to fit residues: 9.8086
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  : 1.042 
-------------------------------------------------------------------------------
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 57 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9990
   chunk 50 optimal weight:    0.5980
   chunk 32 optimal weight:    0.5980
   chunk 75 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0570
   chunk 3 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 69 optimal weight:    0.1980
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.4298

-------------------------------------------------------------------------------
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 = 0.4047 r_free = 0.4047 target = 0.075210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.060834 restraints weight = 90439.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.063285 restraints weight = 36450.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.064755 restraints weight = 20039.490|
|-----------------------------------------------------------------------------|
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7192
moved from start:          0.2819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6757  Z= 0.096
  Angle     :  0.533   9.637   9242  Z= 0.262
  Chirality :  0.040   0.156   1073
  Planarity :  0.003   0.041   1160
  Dihedral  :  5.266  46.575   1193
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  : 10.31 %
    Favored  : 89.14 %
  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:  1.21 (0.30), residues: 801
  helix: -1.03 (0.65), residues: 57
  sheet:  1.42 (0.26), residues: 349
  loop :  0.63 (0.33), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP H 513 
 HIS   0.002   0.000   HIS X 316 
 PHE   0.007   0.001   PHE X 501 
 TYR   0.017   0.001   TYR X 307 
 ARG   0.002   0.000   ARG X 390 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00440 (    6)
  link_NAG-ASN         : angle       3.56818 (   18)
  link_ALPHA1-4        : bond        0.00261 (    1)
  link_ALPHA1-4        : angle       1.59221 (    3)
  link_ALPHA1-6        : bond        0.00380 (    2)
  link_ALPHA1-6        : angle       1.54416 (    6)
  link_BETA1-4         : bond        0.00268 (    5)
  link_BETA1-4         : angle       1.55763 (   15)
  link_ALPHA1-3        : bond        0.00893 (    2)
  link_ALPHA1-3        : angle       1.68357 (    6)
  hydrogen bonds       : bond        0.02588 (  260)
  hydrogen bonds       : angle       4.49785 (  747)
  SS BOND              : bond        0.00213 (   10)
  SS BOND              : angle       2.72177 (   20)
  covalent geometry    : bond        0.00218 ( 6731)
  covalent geometry    : angle       0.48711 ( 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
  20 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 16
  time to evaluate  : 1.104 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 4
  outliers final: 3
  residues processed: 19
  average time/residue: 0.2518
  time to fit residues: 8.4918
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  : 0.956 
-------------------------------------------------------------------------------
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 59 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   chunk 71 optimal weight:    0.6980
   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:    6.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    1.5186

-------------------------------------------------------------------------------
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 = 0.3982 r_free = 0.3982 target = 0.073024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.058088 restraints weight = 96476.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.060494 restraints weight = 39760.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.061915 restraints weight = 22451.156|
|-----------------------------------------------------------------------------|
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7320
moved from start:          0.3424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   6757  Z= 0.218
  Angle     :  0.615   6.715   9242  Z= 0.305
  Chirality :  0.040   0.140   1073
  Planarity :  0.004   0.041   1160
  Dihedral  :  5.622  50.309   1193
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  : 10.45 %
    Favored  : 88.72 %
  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:  0.77 (0.29), residues: 801
  helix: -1.34 (0.65), residues: 57
  sheet:  1.12 (0.26), residues: 349
  loop :  0.36 (0.33), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP R 110 
 HIS   0.006   0.001   HIS X 316 
 PHE   0.015   0.002   PHE R  84 
 TYR   0.023   0.002   TYR X 307 
 ARG   0.011   0.001   ARG X 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00730 (    6)
  link_NAG-ASN         : angle       3.54492 (   18)
  link_ALPHA1-4        : bond        0.00336 (    1)
  link_ALPHA1-4        : angle       2.17019 (    3)
  link_ALPHA1-6        : bond        0.00333 (    2)
  link_ALPHA1-6        : angle       1.45087 (    6)
  link_BETA1-4         : bond        0.00591 (    5)
  link_BETA1-4         : angle       1.95918 (   15)
  link_ALPHA1-3        : bond        0.00742 (    2)
  link_ALPHA1-3        : angle       1.64901 (    6)
  hydrogen bonds       : bond        0.03154 (  260)
  hydrogen bonds       : angle       4.86688 (  747)
  SS BOND              : bond        0.00528 (   10)
  SS BOND              : angle       2.08712 (   20)
  covalent geometry    : bond        0.00463 ( 6731)
  covalent geometry    : angle       0.57926 ( 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
  20 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 14
  time to evaluate  : 0.993 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 6
  outliers final: 5
  residues processed: 19
  average time/residue: 0.2414
  time to fit residues: 8.3145
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  : 1.061 
-------------------------------------------------------------------------------
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 61 optimal weight:    0.4980
   chunk 24 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 8 optimal weight:    7.9990
   chunk 36 optimal weight:    0.9980
   chunk 67 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   overall best weight:    1.4986

-------------------------------------------------------------------------------
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 = 0.3968 r_free = 0.3968 target = 0.072379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.057602 restraints weight = 94071.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.059991 restraints weight = 38124.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.061443 restraints weight = 21324.954|
|-----------------------------------------------------------------------------|
r_work (final): 0.3681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7297
moved from start:          0.3815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   6757  Z= 0.176
  Angle     :  0.576   6.623   9242  Z= 0.287
  Chirality :  0.040   0.150   1073
  Planarity :  0.004   0.041   1160
  Dihedral  :  5.441  49.631   1193
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  : 10.31 %
    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:  0.69 (0.30), residues: 801
  helix: -1.42 (0.65), residues: 57
  sheet:  1.01 (0.26), residues: 348
  loop :  0.37 (0.33), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 110 
 HIS   0.005   0.001   HIS H 525 
 PHE   0.009   0.001   PHE X 500 
 TYR   0.010   0.001   TYR X 307 
 ARG   0.004   0.001   ARG X 437 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00634 (    6)
  link_NAG-ASN         : angle       3.59409 (   18)
  link_ALPHA1-4        : bond        0.00106 (    1)
  link_ALPHA1-4        : angle       1.76811 (    3)
  link_ALPHA1-6        : bond        0.00430 (    2)
  link_ALPHA1-6        : angle       1.45123 (    6)
  link_BETA1-4         : bond        0.00287 (    5)
  link_BETA1-4         : angle       1.58468 (   15)
  link_ALPHA1-3        : bond        0.00784 (    2)
  link_ALPHA1-3        : angle       1.49503 (    6)
  hydrogen bonds       : bond        0.03007 (  260)
  hydrogen bonds       : angle       4.92203 (  747)
  SS BOND              : bond        0.00208 (   10)
  SS BOND              : angle       1.69317 (   20)
  covalent geometry    : bond        0.00374 ( 6731)
  covalent geometry    : angle       0.54296 ( 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
  22 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 16
  time to evaluate  : 1.095 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 6
  outliers final: 5
  residues processed: 21
  average time/residue: 0.2501
  time to fit residues: 9.3889
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  : 1.113 
-------------------------------------------------------------------------------
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 63 optimal weight:    0.5980
   chunk 66 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9990
   chunk 59 optimal weight:    0.7980
   chunk 77 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3980 r_free = 0.3980 target = 0.072894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.058116 restraints weight = 94486.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.060529 restraints weight = 38706.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.061974 restraints weight = 21706.101|
|-----------------------------------------------------------------------------|
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7305
moved from start:          0.3891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6757  Z= 0.134
  Angle     :  0.561   7.984   9242  Z= 0.278
  Chirality :  0.040   0.150   1073
  Planarity :  0.004   0.041   1160
  Dihedral  :  5.286  48.365   1193
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  : 10.45 %
    Favored  : 88.72 %
  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 (0.30), residues: 801
  helix: -1.28 (0.65), residues: 57
  sheet:  1.08 (0.26), residues: 344
  loop :  0.42 (0.33), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP X 513 
 HIS   0.003   0.001   HIS H 525 
 PHE   0.006   0.001   PHE X 500 
 TYR   0.016   0.001   TYR X 307 
 ARG   0.003   0.000   ARG X 390 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00501 (    6)
  link_NAG-ASN         : angle       3.55311 (   18)
  link_ALPHA1-4        : bond        0.00092 (    1)
  link_ALPHA1-4        : angle       1.73832 (    3)
  link_ALPHA1-6        : bond        0.00352 (    2)
  link_ALPHA1-6        : angle       1.48080 (    6)
  link_BETA1-4         : bond        0.00263 (    5)
  link_BETA1-4         : angle       1.52571 (   15)
  link_ALPHA1-3        : bond        0.00704 (    2)
  link_ALPHA1-3        : angle       1.49040 (    6)
  hydrogen bonds       : bond        0.02781 (  260)
  hydrogen bonds       : angle       4.79771 (  747)
  SS BOND              : bond        0.00178 (   10)
  SS BOND              : angle       2.36629 (   20)
  covalent geometry    : bond        0.00297 ( 6731)
  covalent geometry    : angle       0.52139 ( 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
  22 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 16
  time to evaluate  : 1.116 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 6
  outliers final: 4
  residues processed: 20
  average time/residue: 0.2593
  time to fit residues: 9.3205
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  : 1.104 
-------------------------------------------------------------------------------
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 35 optimal weight:    0.0370
   chunk 42 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0070
   chunk 49 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   chunk 1 optimal weight:    6.9990
   chunk 33 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9990
   chunk 73 optimal weight:    0.9990
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.5280

-------------------------------------------------------------------------------
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 = 0.3989 r_free = 0.3989 target = 0.073205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.058558 restraints weight = 92537.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.060979 restraints weight = 37139.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.062442 restraints weight = 20637.952|
|-----------------------------------------------------------------------------|
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7261
moved from start:          0.3898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6757  Z= 0.102
  Angle     :  0.531   6.891   9242  Z= 0.261
  Chirality :  0.040   0.164   1073
  Planarity :  0.004   0.040   1160
  Dihedral  :  4.958  45.923   1193
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  : 10.31 %
    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:  0.99 (0.30), residues: 801
  helix: -1.07 (0.66), residues: 57
  sheet:  1.19 (0.26), residues: 351
  loop :  0.56 (0.34), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP X 513 
 HIS   0.002   0.001   HIS R 108 
 PHE   0.006   0.001   PHE H 500 
 TYR   0.012   0.001   TYR X 307 
 ARG   0.003   0.000   ARG X 437 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00444 (    6)
  link_NAG-ASN         : angle       3.45956 (   18)
  link_ALPHA1-4        : bond        0.00100 (    1)
  link_ALPHA1-4        : angle       1.58965 (    3)
  link_ALPHA1-6        : bond        0.00394 (    2)
  link_ALPHA1-6        : angle       1.46838 (    6)
  link_BETA1-4         : bond        0.00259 (    5)
  link_BETA1-4         : angle       1.42169 (   15)
  link_ALPHA1-3        : bond        0.00686 (    2)
  link_ALPHA1-3        : angle       1.43448 (    6)
  hydrogen bonds       : bond        0.02584 (  260)
  hydrogen bonds       : angle       4.63984 (  747)
  SS BOND              : bond        0.00306 (   10)
  SS BOND              : angle       1.99838 (   20)
  covalent geometry    : bond        0.00229 ( 6731)
  covalent geometry    : angle       0.49441 ( 9174)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4530.79 seconds
wall clock time: 78 minutes 31.90 seconds (4711.90 seconds total)